diff --git a/.github/renovate.json5 b/.github/renovate.json5 index eacaed1524b..430da386501 100644 --- a/.github/renovate.json5 +++ b/.github/renovate.json5 @@ -23,7 +23,7 @@ "(^|/)action\\.ya?ml$" ], "matchStrings": [ - "# renovate: datasource=(?[a-z-.]+?) depName=(?[^\\s]+?)(?: (?:lookupName|packageName)=(?[^\\s]+?))?(?: versioning=(?[^\\s]+?))?(?: extractVersion=(?[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?.+?)[\"']?\\s" + "# renovate: datasource=(?[a-z-.]+?) depName=(?[^\\s]+?)(?: (?:lookupName|packageName)=(?[^\\s]+?))?(?: versioning=(?[^\\s]+?))?(?: extractVersion=(?[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VER(SION)?\\s*:\\s*[\"']?(?.+?)[\"']?\\s" ] } ] diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml index 052b00b9023..44f3d877b4f 100644 --- a/.github/workflows/gpu-tests.yml +++ b/.github/workflows/gpu-tests.yml @@ -35,7 +35,7 @@ env: NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver - NXF_VERSION: "24.10.1" + NXF_VER: "24.10.1" jobs: nf-test-changes: diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 21f25628b6c..e89c7afcc44 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -32,7 +32,7 @@ env: NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver - NXF_VERSION: "24.10.1" + NXF_VER: "24.10.1" jobs: nf-test: diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 4d4a96d0f38..66112152252 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -29,7 +29,7 @@ env: NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver - NXF_VERSION: "24.10.1" + NXF_VER: "24.10.1" jobs: pytest-changes: @@ -266,7 +266,7 @@ jobs: - name: Setup Nextflow uses: nf-core/setup-nextflow@v2 with: - version: ${{ env.NXF_VERSION }} + version: ${{ env.NXF_VER }} - name: Setup apptainer if: matrix.profile == 'singularity' diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml index 2c04a0355c0..5e734e49db6 100644 --- a/.github/workflows/wave.yml +++ b/.github/workflows/wave.yml @@ -15,7 +15,7 @@ env: # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver NFT_VER: "0.9.2" # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver - NXF_VERSION: "24.10.1" + NXF_VER: "24.10.1" jobs: generate-matrix: diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf index 861f7045a14..12062f75c56 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf +++ b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process GATK4_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap index 93a87cc39eb..07101dc9bfd 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap @@ -32,7 +32,7 @@ ], "3": [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ], "bai": [ [ @@ -54,27 +54,27 @@ ], "versions": [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T13:19:33.815262" + "timestamp": "2024-10-31T10:28:22.832793576" }, "versions": { "content": [ [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T13:19:18.103325" + "timestamp": "2024-10-31T10:28:10.146204216" }, "cram_name": { "content": [ diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf index dfe9dc27a09..1f0263758fa 100644 --- a/modules/nf-core/gatk4/annotateintervals/main.nf +++ b/modules/nf-core/gatk4/annotateintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap index 749f6fb6f13..3b06f09771a 100644 --- a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:07:36.32193" + "timestamp": "2024-10-31T10:29:29.006068994" }, "homo_sapiens genome [interval_list]": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:12.533176" + "timestamp": "2024-10-31T10:30:08.763305448" }, "homo_sapiens genome multi-interval [bed]": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:07:54.643276" + "timestamp": "2024-10-31T10:29:48.403638052" }, "homo_sapiens genome [interval_list] mappable_regions": { "content": [ @@ -117,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -129,28 +129,28 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:31.311782" + "timestamp": "2024-10-31T10:30:23.256626974" }, "homo_sapiens genome [bed] - stub": { "content": [ [ "test.tsv", - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:09:04.54745" + "timestamp": "2024-10-31T10:30:52.179735439" }, "homo_sapiens genome [interval_list] duplication_regions": { "content": [ @@ -165,7 +165,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -177,14 +177,14 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:49.684766" + "timestamp": "2024-10-31T10:30:37.398809104" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 4e91c311b0e..5267454e8ed 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index 19b37d0636d..427cbddb8d0 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ @@ -28,15 +28,15 @@ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:25:00.314573" + "timestamp": "2024-10-31T10:32:45.888751339" }, "sarscov2 - bam - intervals": { "content": [ @@ -46,48 +46,48 @@ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:48.144461" + "timestamp": "2024-10-31T10:31:59.340916681" }, "sarscov2 - cram": { "content": [ [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:22:09.308602" + "timestamp": "2024-10-31T10:32:16.162569909" }, "test.cram": { "content": [ @@ -114,7 +114,7 @@ ] ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ @@ -128,15 +128,15 @@ ] ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:24:52.761169" + "timestamp": "2024-10-31T10:32:34.223186142" }, "sarscov2 - bam": { "content": [ @@ -146,35 +146,35 @@ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:28.719225" + "timestamp": "2024-10-31T10:31:44.601557038" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 047321b8e9e..c8ea3da5bf2 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYVQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap index ad2fe8be65a..1f3e97cbfdc 100644 --- a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap @@ -22,14 +22,14 @@ "versions": { "content": [ [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:00:49.353138" + "timestamp": "2024-10-31T10:33:41.980566137" }, "human - vcf - stub": { "content": [ @@ -51,7 +51,7 @@ ] ], "2": [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ], "tbi": [ [ @@ -70,26 +70,26 @@ ] ], "versions": [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:01:24.370421" + "timestamp": "2024-10-31T10:34:08.561335315" }, "versions_allelspecific": { "content": [ [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:01:08.104194" + "timestamp": "2024-10-31T10:33:56.418381574" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf index cb9083e0761..3f09bffe34d 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf +++ b/modules/nf-core/gatk4/asereadcounter/main.nf @@ -4,8 +4,8 @@ process GATK4_ASEREADCOUNTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bai), path(vcf), path(tbi) @@ -53,7 +53,6 @@ process GATK4_ASEREADCOUNTER { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap index cb2740864b2..afaec52efe4 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap +++ b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,d567b20620f5adf0829cc4b4adb9f6ff" + "versions.yml:md5,64995de5e01e2d49fccd2b97df276d01" ], "csv": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,d567b20620f5adf0829cc4b4adb9f6ff" + "versions.yml:md5,64995de5e01e2d49fccd2b97df276d01" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T10:03:42.158801" + "timestamp": "2024-10-31T10:35:00.386844997" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 1a299862657..4fbf02d606a 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap index 8291304ba87..c3fca758eb8 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:00.04396" + "timestamp": "2024-10-31T10:36:20.634357503" }, "sarscov2 - bam - intervals": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -55,15 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:17.899391" + "timestamp": "2024-10-31T10:35:55.223087741" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -77,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -88,15 +88,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:47.770383" + "timestamp": "2024-10-31T10:36:10.08523788" }, "homo_sapiens - cram ": { "content": [ @@ -110,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -121,15 +121,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:42.135898" + "timestamp": "2024-10-31T10:36:42.285370441" }, "sarscov2 - bam": { "content": [ @@ -143,7 +143,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -154,14 +154,14 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:14:57.629443" + "timestamp": "2024-10-31T10:35:41.89476551" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 68863d677d7..89960e04cac 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -1,11 +1,11 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap index 48c322fd001..6936cf97175 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T14:20:12.168775" + "timestamp": "2024-10-31T10:37:25.720782902" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 1ca3fd9d45f..20fe3c5e139 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,8 +4,8 @@ process GATK4_CALCULATECONTAMINATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap index 5c2930f948f..756c2452f8a 100644 --- a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap @@ -2,38 +2,38 @@ "versions_pair": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:17.057861" + "timestamp": "2024-10-31T10:39:04.844937172" }, "versions": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:07.193762" + "timestamp": "2024-10-31T10:38:50.36175509" }, "versions_segmentation": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:26.99069" + "timestamp": "2024-10-31T10:39:22.516513354" }, "segmentation": { "content": [ @@ -75,7 +75,7 @@ ] ], "2": [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ], "contamination": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:56:14.817045" + "timestamp": "2024-10-31T10:39:40.353818746" }, "human - pileup-table - matched-pair": { "content": [ diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 88e108cb01e..eb16037b876 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap index d0d7b8b9dce..2ece2ae6151 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap @@ -9,14 +9,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:17.584362" + "timestamp": "2024-10-31T10:40:49.021126898" }, "test-gatk4-calibratedragstrmodel-cram": { "content": [ @@ -28,14 +28,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:30.21551" + "timestamp": "2024-10-31T10:41:19.764355383" }, "test-gatk4-calibratedragstrmodel-gzipped-beds": { "content": [ @@ -47,14 +47,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:53.619871" + "timestamp": "2024-10-31T10:42:13.527330586" }, "test-gatk4-calibratedragstrmodel-beds": { "content": [ @@ -66,13 +66,13 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:41.938548" + "timestamp": "2024-10-31T10:41:47.344014169" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/cnnscorevariants/README.md b/modules/nf-core/gatk4/cnnscorevariants/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/cnnscorevariants/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/cnnscorevariants/environment.yml b/modules/nf-core/gatk4/cnnscorevariants/environment.yml new file mode 100644 index 00000000000..da693d88d57 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 92de2267e06..5ff13b41d15 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -28,10 +28,10 @@ process GATK4_CNNSCOREVARIANTS { } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def aligned_input = aligned_input ? "--input $aligned_input" : "" + def aligned_input_cmd = aligned_input ? "--input $aligned_input" : "" def interval_command = intervals ? "--intervals $intervals" : "" - def architecture = architecture ? "--architecture $architecture" : "" - def weights = weights ? "--weights $weights" : "" + def architecture_cmd = architecture ? "--architecture $architecture" : "" + def weights_cmd = weights ? "--weights $weights" : "" def avail_mem = 3072 if (!task.memory) { @@ -48,9 +48,9 @@ process GATK4_CNNSCOREVARIANTS { --output ${prefix}.cnn.vcf.gz \\ --reference $fasta \\ $interval_command \\ - $aligned_input \\ - $architecture \\ - $weights \\ + $aligned_input_cmd \\ + $architecture_cmd \\ + $weights_cmd \\ --tmp-dir . \\ $args @@ -59,4 +59,17 @@ process GATK4_CNNSCOREVARIANTS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.cnn.vcf.gz + touch ${prefix}.cnn.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test new file mode 100644 index 00000000000..db58bf421c1 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test @@ -0,0 +1,77 @@ +nextflow_process { + + name "Test Process GATK4_CNNSCOREVARIANTS" + script "../main.nf" + process "GATK4_CNNSCOREVARIANTS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/cnnscorevariants" + + test("homo sapiens - vcf") { + when { + process { + """ + input_vcf = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), + [], + [] + ] + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + + input = [input_vcf, fasta, fai, dict, [], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + ).match() } + ) + } + + } + + test("homo sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input_vcf = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi", checkIfExists: true), + [], + [] + ] + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + + input = [input_vcf, fasta, fai, dict, [], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap new file mode 100644 index 00000000000..63be00cfee3 --- /dev/null +++ b/modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "homo sapiens - vcf": { + "content": [ + [ + "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" + ], + "34e15624519ba7408d53cb8bb365ffc1", + "test.cnn.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-18T09:39:27.896072791" + }, + "homo sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.cnn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,7e0d98246eb35725469a53e6fb8acfbf" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:46:55.099673108" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 2c545d22432..c742a16b178 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -1,11 +1,11 @@ process GATK4_COLLECTREADCOUNTS { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap index 28a3a6e151b..212f950d28a 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -15,7 +15,7 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ], "hdf5": [ @@ -30,15 +30,15 @@ ] ], "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:58:19.610687" + "timestamp": "2024-10-31T10:44:48.133712731" }, "test-gatk4-collectreadcounts-hdf5": { "content": [ @@ -69,7 +69,7 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ], "hdf5": [ @@ -84,14 +84,14 @@ ] ], "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:58:07.500024" + "timestamp": "2024-10-31T10:44:24.624195466" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 9e6dd4a284b..b29153dc16f 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(site_depth_vcf), path(site_depth_vcf_tbi) diff --git a/modules/nf-core/gatk4/collectsvevidence/meta.yml b/modules/nf-core/gatk4/collectsvevidence/meta.yml index a9d64d30e50..5ee2b975c7f 100644 --- a/modules/nf-core/gatk4/collectsvevidence/meta.yml +++ b/modules/nf-core/gatk4/collectsvevidence/meta.yml @@ -37,8 +37,8 @@ input: pattern: "*.vcf.gz" - site_depth_vcf_tbi: type: file - description: Optional - input VCF TBI of SNPs marking loci for site depths, needed - for the site depths output + description: Optional - input VCF TBI of SNPs marking loci for site depths, + needed for the site depths output pattern: "*.vcf.gz.tbi" - - fasta: type: file diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap index 1f6992b8c64..cca8eea4c05 100644 --- a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap @@ -6,14 +6,14 @@ "chr22\t3320\t+\tchr22\t3482\t-\tnormal", "test.pe.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:51:11.44656" + "timestamp": "2024-10-31T10:46:15.558451518" }, "test-gatk4-collectsvevidence-cram - stub": { "content": [ @@ -61,7 +61,7 @@ ], "6": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ], "paired_end_evidence": [ [ @@ -106,15 +106,15 @@ ] ], "versions": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:36:35.045647" + "timestamp": "2024-10-31T10:46:54.409850619" }, "test-gatk4-collectsvevidence-allele-count": { "content": [ @@ -125,14 +125,14 @@ "chr22\t1981\tnormal\t235\t0\t48\t0", "test.sd.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:48:13.663238" + "timestamp": "2024-10-31T10:46:42.62581769" }, "test-gatk4-collectsvevidence-allele-count - stub": { "content": [ @@ -192,7 +192,7 @@ ] ], "6": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ], "paired_end_evidence": [ [ @@ -249,15 +249,15 @@ ] ], "versions": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:36:43.992644" + "timestamp": "2024-10-31T10:47:05.276032478" }, "test-gatk4-collectsvevidence-bam": { "content": [ @@ -266,13 +266,13 @@ "chr22\t3320\t+\tchr22\t3482\t-\tnormal", "test.pe.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:51:22.087808" + "timestamp": "2024-10-31T10:46:29.443818792" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 56db0c12c86..1528ac735d5 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_COMBINEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap index dfbd1ac1ef7..00aea2bdcca 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ], "combined_gvcf": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:35:25.18434" + "timestamp": "2024-10-31T10:47:56.847188152" }, "test_gatk4_combinegvcfs": { "content": [ @@ -169,13 +169,13 @@ "chr22\t4608\t.\tA\t\t.\t.\tEND=40001\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0" ], [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:41:25.316932" + "timestamp": "2024-10-31T10:47:45.34645647" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 5073ab64200..71c867cc28c 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,8 +4,8 @@ process GATK4_COMPOSESTRTABLEFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap index 02136a8b365..4a62f028b5d 100644 --- a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "genome.zip", [ - "versions.yml:md5,755f9a44a99148151b624d70eb6ce260" + "versions.yml:md5,b70639968daefca28136a26156170e29" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:37:10.366333" + "timestamp": "2024-10-31T10:48:46.420056406" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/condensedepthevidence/main.nf b/modules/nf-core/gatk4/condensedepthevidence/main.nf index a37b6693f39..f1f80715426 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ b/modules/nf-core/gatk4/condensedepthevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_CONDENSEDEPTHEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(depth_evidence), path(depth_evidence_index) diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap index b9dddfbb989..ac0a8fa58fd 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ], "condensed_evidence": [ [ @@ -42,15 +42,15 @@ ] ], "versions": [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:42:07.848497" + "timestamp": "2024-10-31T10:49:51.212441436" }, "test-gatk4-condensdepthevidence": { "content": [ @@ -60,13 +60,13 @@ ], "test.rd.txt.gz.tbi", [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:33:21.910858" + "timestamp": "2024-10-31T10:49:37.340222412" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf index 332f9d9247f..b754b05cc84 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(counts) @@ -42,7 +42,6 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.hdf5 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test new file mode 100644 index 00000000000..f16c2df39d8 --- /dev/null +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test @@ -0,0 +1,102 @@ +nextflow_process { + + name "Test Process GATK4_CREATEREADCOUNTPANELOFNORMALS" + script "../main.nf" + config "./nextflow.config" + process "GATK4_CREATEREADCOUNTPANELOFNORMALS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/preprocessintervals" + tag "gatk4/collectreadcounts" + tag "gatk4/createreadcountpanelofnormals" + + setup { + run("GATK4_PREPROCESSINTERVALS") { + script "../../preprocessintervals/main.nf" + process { + """ + fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() + + input[0] = fasta + input[1] = fai + input[2] = dict + input[3] = [[],[]] + input[4] = [[],[]] + """ + } + } + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map{ meta, list -> list} + input[0] = Channel.of([ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + ], + [ + [ id:'test2', single_end:false ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + ]) + .combine(intervals) + input[1] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta",checkIfExists: true)]).collect() + input[2] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai",checkIfExists: true)]).collect() + input[3] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict",checkIfExists: true)]).collect() + """ + } + } + } + + test("homo sapiens - bam") { + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.pon[0][1]).name + ).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap new file mode 100644 index 00000000000..630cab6ab2c --- /dev/null +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "homo sapiens - bam": { + "content": [ + [ + "versions.yml:md5,3b00a427858f3b991cc03fe6b467fe9d" + ], + "test.hdf5" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T09:28:03.932486659" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3b00a427858f3b991cc03fe6b467fe9d" + ], + "pon": [ + [ + { + "id": "test" + }, + "test.hdf5:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3b00a427858f3b991cc03fe6b467fe9d" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-14T10:57:07.220349234" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/nextflow.config similarity index 67% rename from tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config rename to modules/nf-core/gatk4/createreadcountpanelofnormals/tests/nextflow.config index a8c5250b024..90cfd3c7dc7 100644 --- a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/tests/nextflow.config @@ -1,3 +1,4 @@ +docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b3c1..998622a0658 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -1,11 +1,11 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 16735f9549a..e8a600fd114 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:16:16.34453" + "timestamp": "2024-10-31T10:51:56.155954077" }, "sarscov2 - fasta": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T13:58:25.822068" + "timestamp": "2024-10-31T10:51:45.562993875" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 27a50dc208d..fb6fdf7c04e 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(genomicsdb) @@ -45,4 +45,18 @@ process GATK4_CREATESOMATICPANELOFNORMALS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "${prefix}" | gzip -c > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + + } diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test new file mode 100644 index 00000000000..95cb57240bd --- /dev/null +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process GATK4_CREATESOMATICPANELOFNORMALS" + script "../main.nf" + process "GATK4_CREATESOMATICPANELOFNORMALS" + + tag "modules" + tag "modules_nfcore" + tag "untar" + tag "gatk4" + tag "gatk4/createsomaticpanelofnormals" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [[id:'test'], file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz", checkIfExists: true) ] + """ + } + } + } + + test("homo sapiens - genomicsdb") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() } + ) + } + + } + + test("homo sapiens - genomicsdb - stub") { + + options "-stub" + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap new file mode 100644 index 00000000000..d4da4f2a7da --- /dev/null +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "homo sapiens - genomicsdb": { + "content": [ + [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ], + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T20:27:41.348681175" + }, + "homo sapiens - genomicsdb - stub": { + "content": [ + [ + "versions.yml:md5,672d1b17845a11d8a296d1885f3a9fa4" + ], + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T20:27:58.84258624" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 878e85c6f97..6b3d1ea5191 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_DENOISEREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(counts) @@ -46,7 +46,6 @@ process GATK4_DENOISEREADCOUNTS { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_standardizedCR.tsv diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index f35eb283db4..541e6c61216 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -20,13 +20,13 @@ ] ], [ - "versions.yml:md5,140780e1af7318cc9259b8970bc70c81" + "versions.yml:md5,2e89249bc2ef4e86a3fc59f0913c5525" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:34:12.568925" + "timestamp": "2024-10-31T10:45:25.930205969" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md b/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml new file mode 100644 index 00000000000..1f7d0824620 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index fc98e80e4aa..6edccf6117e 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -3,8 +3,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(counts), path(bed), path(exclude_beds) @@ -20,10 +22,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def intervals = bed ? "--intervals ${bed}" : "" @@ -40,6 +38,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" export OMP_NUM_THREADS=${task.cpus} export MKL_NUM_THREADS=${task.cpus} @@ -62,10 +61,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}-calls diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test new file mode 100644 index 00000000000..a6d0fb7b7e7 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_process { + + name "Test Process GATK4_DETERMINEGERMLINECONTIGPLOIDY" + script "../main.nf" + config "./nextflow.config" + process "GATK4_DETERMINEGERMLINECONTIGPLOIDY" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + + setup { + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) + + ch_input = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true) + ], + ).combine(bed) + + ch_fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + ch_fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + ch_dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() + + input = [ch_input, ch_fasta, ch_fai, ch_dict] + """ + } + } + } + + test("homo sapiens - bam") { + + when { + process { + """ + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'] , tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.calls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.model[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'] , tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap new file mode 100644 index 00000000000..83d018e1edb --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -0,0 +1,77 @@ +{ + "homo sapiens - bam": { + "content": [ + [ + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" + ], + [ + "SAMPLE_0", + "SAMPLE_1" + ], + [ + "contig_ploidy_prior.tsv", + "gcnvkernel_version.json", + "interval_list.tsv", + "mu_mean_bias_j_interval__.tsv", + "mu_psi_j_log__.tsv", + "ploidy_config.json", + "std_mean_bias_j_interval__.tsv", + "std_psi_j_log__.tsv" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-18T10:16:43.182419213" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test-calls:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" + ], + "calls": [ + [ + { + "id": "test" + }, + "test-calls:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "model": [ + [ + { + "id": "test" + }, + "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0dd7026e3a5627b4e3cb464879c9c817" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:23:35.989186048" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config similarity index 54% rename from tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config rename to modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config index a764fa9cc73..2767daca231 100644 --- a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config @@ -1,13 +1,8 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_COLLECTREADCOUNTS { ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" } - - withName: GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT { + withName: GATK4_DETERMINEGERMLINECONTIGPLOIDY { ext.args = "--interval-merging-rule OVERLAPPING_ONLY" } - } diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index e0744e16f7d..9071279577f 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -1,11 +1,11 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input) @@ -46,4 +46,16 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.metrics + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test index e23b65573c9..8552ca47dc2 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test @@ -75,7 +75,7 @@ nextflow_process { } - test("sarscov2 - bam - stub") { + test("homo sapiens - bam - stub") { options "-stub" diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap index bbcef1471e0..73752535e93 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap @@ -3,39 +3,39 @@ "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:41:39.857566" + "timestamp": "2024-10-31T11:01:20.304274717" }, - "sarscov2 - bam - stub": { + "homo sapiens - bam - stub": { "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:27:55.337569" + "timestamp": "2024-11-07T10:17:35.145738139" }, "homo_sapiens - bam": { "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:24:41.460191" + "timestamp": "2024-10-31T11:00:54.378191881" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 452d1ca1f35..e79f847aa04 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -1,11 +1,11 @@ process GATK4_FASTQTOSAM { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap index a4b44520dc5..5c575866db7 100644 --- a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ], "bam": [ [ @@ -24,40 +24,40 @@ ] ], "versions": [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:43:37.316141" + "timestamp": "2024-10-31T11:02:58.024964061" }, "test-gatk4-fastqtosam-single-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:29:12.362942" + "timestamp": "2024-10-31T11:02:34.422399439" }, "test-gatk4-fastqtosam-paired-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:29:22.385798" + "timestamp": "2024-10-31T11:02:47.309600742" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index bf1f3a0e369..ada752daf1d 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -1,11 +1,11 @@ process GATK4_FILTERINTERVALS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap index c9626666948..add6095b313 100644 --- a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + "versions.yml:md5,6fbacd816f4d48eae20f1fd423cb4e56" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + "versions.yml:md5,6fbacd816f4d48eae20f1fd423cb4e56" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:25:35.933532" + "timestamp": "2024-10-31T11:03:52.645895175" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 0532ec02582..d3c5bb5ad78 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERMUTECTCALLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 1c39e3b5d7c..28a63357e7f 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "versions_with-files": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:45:43.679571" + "timestamp": "2024-10-31T11:04:55.625468064" }, "human - vcf - stub": { "content": [ @@ -49,7 +49,7 @@ ] ], "3": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ], "stats": [ [ @@ -76,39 +76,39 @@ ] ], "versions": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:46:32.666273" + "timestamp": "2024-10-31T11:05:33.111919824" }, "versions_use-val": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:46:03.876073" + "timestamp": "2024-10-31T11:05:19.277193087" }, "versions_base": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:47:39.930795" + "timestamp": "2024-10-31T11:04:36.657284567" }, "human - vcf - with-files": { "content": [ diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 05489e179b9..c5249b7a050 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERVARIANTTRANCHES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) @@ -27,7 +27,7 @@ process GATK4_FILTERVARIANTTRANCHES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def resources = resources.collect{"--resource $it"}.join(' ') + def resource_list = resources.collect{"--resource $it"}.join(' ') def avail_mem = 3072 if (!task.memory) { @@ -39,7 +39,7 @@ process GATK4_FILTERVARIANTTRANCHES { gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ FilterVariantTranches \\ --variant $vcf \\ - $resources \\ + $resource_list \\ --output ${prefix}.filtered.vcf.gz \\ --tmp-dir . \\ $args @@ -49,4 +49,17 @@ process GATK4_FILTERVARIANTTRANCHES { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test new file mode 100644 index 00000000000..c315ed8fc01 --- /dev/null +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test @@ -0,0 +1,78 @@ +nextflow_process { + + name "Test Process GATK4_FILTERVARIANTTRANCHES" + script "../main.nf" + config "./nextflow.config" + process "GATK4_FILTERVARIANTTRANCHES" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/filtervarianttranches" + + test("homo sapiens - vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), + [] + ] + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + ).match() + } + ) + } + + } + + test("homo sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true), + [] + ] + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap new file mode 100644 index 00000000000..8bc251b61cf --- /dev/null +++ b/modules/nf-core/gatk4/filtervarianttranches/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "homo sapiens - vcf": { + "content": [ + [ + "versions.yml:md5,bad82b4b3eb370f70925cc069b16b63a" + ], + "test.filtered.vcf.gz", + "test.filtered.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T14:45:11.404254527" + }, + "homo sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,bad82b4b3eb370f70925cc069b16b63a" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,bad82b4b3eb370f70925cc069b16b63a" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T14:18:50.66032726" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config b/modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config similarity index 100% rename from tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config rename to modules/nf-core/gatk4/filtervarianttranches/tests/nextflow.config diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 79667a29948..fdc5a2a723d 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -1,11 +1,11 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap index bc5d4bd1332..e792d07ec56 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ], "table": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:22:34.490694" + "timestamp": "2024-10-31T11:07:33.025431761" }, "test-gatk4-gatherbqsrreports": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ], "table": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:22:10.552951" + "timestamp": "2024-10-31T11:07:09.791064374" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index bcafd544b43..af397a1a2dc 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap index fd9f2583440..e7094d73f4b 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ], "table": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:44:42.759098" + "timestamp": "2024-10-31T11:08:38.118444526" }, "test-gatk4-gatherpileupsummaries": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ], "table": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:18:40.835226" + "timestamp": "2024-10-31T11:08:17.759423015" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 6f1d4c53709..90f1200dc7a 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -1,11 +1,11 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap index 55ced0d8802..cb47a432c9e 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf", [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:42:51.836379" + "timestamp": "2024-10-31T11:09:55.9195126" }, "test_gatk4_genomicsdbimport_create_genomicsdb": { "content": [ @@ -22,14 +22,14 @@ "vidmap.json" ], [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:42:36.846239" + "timestamp": "2024-10-31T11:09:25.302350893" }, "test_gatk4_genomicsdbimport_update_genomicsdb": { "content": [ @@ -41,14 +41,14 @@ "vidmap.json" ], [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:43:09.00769" + "timestamp": "2024-10-31T11:10:13.206208761" }, "test_gatk4_genomicsdbimport_stub": { "content": [ @@ -68,7 +68,7 @@ ], "3": [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ], "genomicsdb": [ [ @@ -85,14 +85,14 @@ ], "versions": [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:43:20.921712" + "timestamp": "2024-10-31T11:10:36.510210505" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index f180f74975c..dc2813a350c 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -1,11 +1,11 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" - label 'process_high' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap index 1621618e7a9..30e2dc1cc6a 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap @@ -18,14 +18,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:24.926097884" + "timestamp": "2024-10-31T11:16:45.625453031" }, "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": { "content": [ @@ -46,14 +46,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:26:24.426228557" + "timestamp": "2024-10-31T11:15:55.296562046" }, "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": { "content": [ @@ -74,14 +74,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:04.179308513" + "timestamp": "2024-10-31T11:16:30.471742609" }, "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": { "content": [ @@ -102,14 +102,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:26:43.9088684" + "timestamp": "2024-10-31T11:16:13.266019505" }, "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": { "content": [ @@ -131,7 +131,7 @@ ] ], "2": [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ], "tbi": [ [ @@ -150,15 +150,15 @@ ] ], "versions": [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:19:57.615552867" + "timestamp": "2024-10-31T11:17:19.342242664" }, "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": { "content": [ @@ -179,13 +179,13 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:46.189794941" + "timestamp": "2024-10-31T11:17:01.475664058" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/germlinecnvcaller/README.md b/modules/nf-core/gatk4/germlinecnvcaller/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/germlinecnvcaller/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml new file mode 100644 index 00000000000..1f7d0824620 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 90aa7e47113..e8afb1fbf1a 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -2,8 +2,10 @@ process GATK4_GERMLINECNVCALLER { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) @@ -18,10 +20,6 @@ process GATK4_GERMLINECNVCALLER { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def intervals_command = intervals ? "--intervals ${intervals}" : "" @@ -38,6 +36,7 @@ process GATK4_GERMLINECNVCALLER { } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" export OMP_NUM_THREADS=${task.cpus} export MKL_NUM_THREADS=${task.cpus} @@ -58,10 +57,6 @@ process GATK4_GERMLINECNVCALLER { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p ${prefix}-cnv-calls/${prefix}-calls diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test new file mode 100644 index 00000000000..d14ef9a0ff3 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -0,0 +1,126 @@ +nextflow_process { + + name "Test Process GATK4_GERMLINECNVCALLER" + script "../main.nf" + config "./nextflow.config" + process "GATK4_GERMLINECNVCALLER" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/bedtointervallist" + tag "gatk4/germlinecnvcaller" + + setup { + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + input[0] = Channel.of( + [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + ]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) + input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + + """ + } + } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY") { + script "../../determinegermlinecontigploidy/main.nf" + process { + """ + bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + input[0] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + """ + } + } + } + + test("homo sapiens - bam") { + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap new file mode 100644 index 00000000000..bbec501bf87 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "homo sapiens - bam": { + "content": [ + [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + [ + "SAMPLE_0", + "SAMPLE_1", + "calling_config.json", + "denoising_config.json", + "gcnvkernel_version.json", + "interval_list.tsv" + ], + [ + "calling_config.json", + "denoising_config.json", + "gcnvkernel_version.json", + "interval_list.tsv", + "log_q_tau_tk.tsv", + "mu_W_tu.tsv", + "mu_ard_u_interval__.tsv", + "mu_log_mean_bias_t.tsv", + "mu_psi_t_log__.tsv", + "std_W_tu.tsv", + "std_ard_u_interval__.tsv", + "std_log_mean_bias_t.tsv", + "std_psi_t_log__.tsv" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-18T08:51:49.791400262" + }, + "homo sapiens - bam - stub": { + "content": [ + [ + "versions.yml:md5,73418764ce886774da2a240630f45aff" + ], + [ + + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-18T08:52:19.983061924" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config b/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config new file mode 100644 index 00000000000..d1b64bf4f03 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS*' { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_GERMLINECNVCALLER' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" + } +} diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 43611271e01..41fd3128118 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GETPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap index d9304bcdc5c..e44c13bad89 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:18:25.186463" + "timestamp": "2024-10-31T11:19:28.038865911" }, "human - bam": { "content": [ @@ -40,30 +40,30 @@ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T14:14:59.7414" + "timestamp": "2024-10-31T11:18:47.633313304" }, "human - cram": { "content": [ @@ -73,29 +73,29 @@ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T14:15:25.680928" + "timestamp": "2024-10-31T11:19:14.207172594" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index b2aff48969e..1ef76789de5 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -1,11 +1,11 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 0203fcfcf48..e3ba2bdfa96 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -4,55 +4,55 @@ "test_cram.vcf.gz", "test_cram.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:36:54.158605" + "timestamp": "2024-10-31T11:20:32.392608448" }, "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": { "content": [ "test_cram_sites.vcf.gz", "test_cram_sites.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:37:13.77024" + "timestamp": "2024-10-31T11:20:49.012555768" }, "homo_sapiens - [bam, bai] - fasta - fai - dict": { "content": [ "test_bam.vcf.gz", "test_bam.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:36:34.77631" + "timestamp": "2024-10-31T11:20:09.342159899" }, "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": { "content": [ "test_cram_sites_dragstr.vcf.gz", "test_cram_sites_dragstr.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:37:32.967085" + "timestamp": "2024-10-31T11:21:06.551678783" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index b1a2698c263..6993537fba0 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,8 +4,8 @@ process GATK4_INDEXFEATUREFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap index fc19333634f..788b9290b87 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "test_gatk4_indexfeaturefile_vcf": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:20.602472" + "timestamp": "2024-10-31T11:22:21.619530121" }, "geneome.bed.idx": { "content": [ @@ -53,7 +53,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -64,15 +64,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:03.058351" + "timestamp": "2024-10-31T11:22:06.537858152" }, "test_gatk4_indexfeaturefile_vcf_gz": { "content": [ @@ -86,7 +86,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -97,15 +97,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:51.861697" + "timestamp": "2024-10-31T11:22:37.41693965" }, "test.genome.vcf.idx": { "content": [ @@ -120,13 +120,13 @@ "test_gatk4_indexfeaturefile_bed": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:56:46.885162" + "timestamp": "2024-10-31T11:21:52.805375486" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 2f6893c0caf..f3cb758006a 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOBED { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) @@ -40,4 +40,16 @@ process GATK4_INTERVALLISTTOBED { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test new file mode 100644 index 00000000000..33bf46fbf10 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process GATK4_INTERVALLISTTOBED" + script "../main.nf" + process "GATK4_INTERVALLISTTOBED" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/intervallisttobed" + + test("homo sapiens - bed") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap new file mode 100644 index 00000000000..0664f5e913f --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttobed/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "homo sapiens - bed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,9046675d01199fbbee79f2bc1c5dce52" + ] + ], + "1": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,9046675d01199fbbee79f2bc1c5dce52" + ] + ], + "versions": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:44:42.715318379" + }, + "homo sapiens - bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,27876d5035fa3f6d4750152ed4033259" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T13:45:01.440631153" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 400fa0380e7..bf20d4c9372 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -1,11 +1,11 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 7718ed00382..3be7acaa3ea 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -16,7 +16,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -32,15 +32,15 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T21:26:22.252885" + "timestamp": "2024-10-31T10:37:46.848386632" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -75,14 +75,14 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:15:11.772344" + "timestamp": "2024-10-31T10:38:00.631338482" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index a61b292812e..86e7daaa6c6 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap index b829bd9c4aa..638e058359c 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap @@ -9,13 +9,13 @@ "CAA\tTTG\t0.0\t3.4445551925564533E-6\t3.435193155024585E-6\t5.139879646597498E-6\t0.0\t3.4674461103560476E-6\t3.428570449688764E-6\t6.343168047383713E-6\t0.9945238954147358\t1.3629167993931722E-4\t0.0052793454402581125\t3.5208652465150646E-5\t29263\t197" ], [ - "versions.yml:md5,88928ff140a0967e574e66944fd2a2f2" + "versions.yml:md5,e8e087001bd49c02f325e90b1fbeb44d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:16:08.296564" + "timestamp": "2024-10-31T11:24:53.596350009" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index b0bede7093d..6087a41872a 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap index f500c0dcc08..e28a7be77b0 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap @@ -4,27 +4,27 @@ "85745045e9c55d3846d80bfde08a7d34", "test.normalised.vcf.gz.tbi", [ - "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + "versions.yml:md5,b8e7f53a1e802cf29ff86c9d1aaae5da" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:09:35.03744" + "timestamp": "2024-10-31T11:25:49.57287314" }, "test-gatk4-leftalignandtrimvariants-interval": { "content": [ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", "test.normalised.vcf.gz.tbi", [ - "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + "versions.yml:md5,b8e7f53a1e802cf29ff86c9d1aaae5da" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:11:42.893725" + "timestamp": "2024-10-31T11:25:35.479943622" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 3c73c17e433..ec65c32da48 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,8 +1,15 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 + # renovate: datasource=conda depName=bioconda/htslib - bioconda::htslib=1.19.1 + # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index baadefef41f..cf770308d59 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -1,6 +1,6 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 0085026c8e5..69027e05305 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEBAMALIGNMENT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap index 719a7bb3311..476eecdfd08 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ], "bam": [ [ @@ -22,27 +22,27 @@ ] ], "versions": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:02:15.41024" + "timestamp": "2024-10-31T11:29:07.319519362" }, "test-gatk4-mergebamalignment": { "content": [ "30c325e1e032eb1782a280d34c0fb1c7", [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:02:08.379035" + "timestamp": "2024-10-31T11:28:55.287907787" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 06bce31e31b..e6ddc6994c1 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEMUTECTSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(stats) @@ -19,7 +19,7 @@ process GATK4_MERGEMUTECTSTATS { script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def input_list = stats.collect{ "--stats ${it}"}.join(' ') def avail_mem = 3072 diff --git a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap index d0279f272e4..77da5d78203 100644 --- a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:13:56.2195" + "timestamp": "2024-10-31T11:29:44.84165293" }, "human - stats,tsv - stub": { "content": [ @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ], "stats": [ [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:14:10.058769" + "timestamp": "2024-10-31T11:29:54.48600467" }, "human - stats, tsv": { "content": [ diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 9e8d43915cc..1752f48a604 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -1,11 +1,11 @@ process GATK4_MERGEVCFS { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index 77ace10a21b..343fff68c97 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs") @@ -48,6 +49,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict") @@ -75,6 +77,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict_stub") diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap index 62cceed57bf..5fab6dca1ba 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -1,35 +1,44 @@ { "test_gatk4_mergevcfs_no_dict_stub": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:57:40.784590995" + "timestamp": "2024-11-07T08:29:25.813956308" }, "test_gatk4_mergevcfs": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:56:42.178255913" + "timestamp": "2024-11-07T08:28:42.580265083" }, "test_gatk4_mergevcfs_no_dict": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:57:11.404322124" + "timestamp": "2024-11-07T08:29:12.795329336" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 79d8d2826ca..3ac374e0356 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -1,11 +1,11 @@ process GATK4_MUTECT2 { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index f047af19dd9..b37450f4f47 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -14,14 +14,14 @@ "test.f1r2.tar.gz" ], [ - "h" + "w" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-21T10:14:45.599103891" + "timestamp": "2024-10-31T11:49:16.64829295" }, "generate_pon": { "content": [ @@ -43,14 +43,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:57:18.264453766" + "timestamp": "2024-10-31T11:48:44.796786166" }, "mitochondria": { "content": [ @@ -72,14 +72,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T16:05:47.668766905" + "timestamp": "2024-10-31T11:49:03.399442766" }, "cram_input": { "content": [ @@ -101,14 +101,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:52:27.894730554" + "timestamp": "2024-10-31T11:45:49.212101867" }, "tumor_single": { "content": [ @@ -130,14 +130,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:43:28.935723443" + "timestamp": "2024-10-31T11:42:47.335589964" }, "tumor_normal_pair": { "content": [ @@ -161,14 +161,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:31:31.913366311" + "timestamp": "2024-10-31T11:36:10.506528759" }, "tumor_normal_pair_f1r2": { "content": [ @@ -192,13 +192,13 @@ "test.f1r2.tar.gz" ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-21T09:45:52.321385704" + "timestamp": "2024-10-31T11:39:21.909639821" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md deleted file mode 100644 index c6a4545655a..00000000000 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml new file mode 100644 index 00000000000..1f7d0824620 --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index 73d4a715877..8bb7420d3f5 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -2,8 +2,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(calls), path(model), path(ploidy) @@ -18,10 +20,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def calls_command = calls ? calls.collect{"--calls-shard-path $it"}.join(' ') : "" @@ -30,18 +28,20 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK GermlineCNVCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + log.info '[GATK PostProcessGermlineCnvCalls] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = (task.memory.mega*0.8).intValue() } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ PostprocessGermlineCNVCalls \\ $calls_command \\ $model_command \\ $ploidy_command \\ + $args \\ --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\ --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\ --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz @@ -53,10 +53,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_genotyped_intervals.vcf.gz diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test new file mode 100644 index 00000000000..6de037b2567 --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -0,0 +1,154 @@ +nextflow_process { + + name "Test Process GATK4_POSTPROCESSGERMLINECNVCALLS" + script "../main.nf" + config "./nextflow.config" + process "GATK4_POSTPROCESSGERMLINECNVCALLS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/bedtointervallist" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/germlinecnvcaller" + tag "gatk4/postprocessgermlinecnvcalls" + + setup { + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + intervals = [[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] + dict = [ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] + + input = [intervals, dict] + """ + } + } + run("GATK4_COLLECTREADCOUNTS"){ + script "../../collectreadcounts/main.nf" + process { + """ + input_bam = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + ]) + + fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() + + input = [input_bam, fasta, fai, dict] + """ + } + } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY", alias: "GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT") { + script "../../determinegermlinecontigploidy/main.nf" + process { + """ + bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + input = [ + GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), + [[],[]], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + ] + """ + } + } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_COHORT") { + script "../../germlinecnvcaller/main.nf" + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) + """ + } + } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_CASE") { + script "../../germlinecnvcaller/main.nf" + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .first() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) + """ + } + } + } + + test("homo sapiens - counts") { + + when { + process { + """ + input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.intervals[0][1]).name, + file(process.out.segments[0][1]).name, + file(process.out.denoised[0][1]).name, + ).match() } + ) + } + + } + + test("homo sapiens - counts - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.intervals[0][1]).name, + file(process.out.segments[0][1]).name, + file(process.out.denoised[0][1]).name, + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap new file mode 100644 index 00000000000..e79b68ae941 --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -0,0 +1,32 @@ +{ + "homo sapiens - counts - stub": { + "content": [ + [ + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" + ], + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-13T13:16:30.579209181" + }, + "homo sapiens - counts": { + "content": [ + [ + "versions.yml:md5,a9e7784f4aa4ec825d4f2b30e97ab05a" + ], + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-13T13:15:53.006230234" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config similarity index 82% rename from tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config rename to modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config index 00adcaaa6bd..81566d90efa 100644 --- a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config @@ -1,22 +1,15 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'GATK4_COLLECTREADCOUNTS*' { ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" } - withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT' { ext.args = "--interval-merging-rule OVERLAPPING_ONLY" ext.prefix = "ploidy" } - withName: 'GATK4_GERMLINECNVCALLER_COHORT' { ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" } - withName: 'GATK4_GERMLINECNVCALLER_CASE' { ext.args = "--run-mode CASE" } - } diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index dffc4bb1df8..bab63495898 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -1,11 +1,11 @@ process GATK4_PREPROCESSINTERVALS { tag "$fasta" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap index 5365291dab8..127164975e3 100644 --- a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + "versions.yml:md5,275510c640bbc3050a257bece1e51f85" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + "versions.yml:md5,275510c640bbc3050a257bece1e51f85" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:58:51.314382" + "timestamp": "2024-10-31T11:55:38.222687003" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index f97180adc24..3f27661974b 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap index 7f1266f2641..b847f44a910 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -9,32 +9,32 @@ ], [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + "versions.yml:md5,b14bcdd8d9bfcf5b7e8f1f58b79fd179" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:48:53.871683" + "timestamp": "2024-10-31T11:56:25.490158526" }, "test-gatk4-printreads-cram": { "content": [ [ ], - "591299d00e262474250c5ccc241bba59", + "d105c4aee01f68ada72b288b1fd72f35", [ ], [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + "versions.yml:md5,b14bcdd8d9bfcf5b7e8f1f58b79fd179" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:42:29.968056" + "timestamp": "2024-10-31T11:56:39.698048025" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 5cf5b05affc..4841391cf7b 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(evidence_files), path(evidence_indices) @@ -63,4 +63,22 @@ process GATK4_PRINTSVEVIDENCE { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def file_name = evidence_files[0].getFileName() + def file_type = file_name =~ ".sr.txt" ? "sr" : + file_name =~ ".pe.txt" ? "pe" : + file_name =~ ".baf.txt" ? "baf" : + file_name =~ ".rd.txt" ? "rd" : + false + """ + echo "" | gzip -c > ${prefix}.${file_type}.txt.gz + touch ${prefix}.${file_type}.txt.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/printsvevidence/meta.yml b/modules/nf-core/gatk4/printsvevidence/meta.yml index 3e3ad72d58e..07ea1223fd0 100644 --- a/modules/nf-core/gatk4/printsvevidence/meta.yml +++ b/modules/nf-core/gatk4/printsvevidence/meta.yml @@ -70,8 +70,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.txt.gz.tbi": type: file - description: The index file of the output compressed text file containing the discordant read - pairs or the soft clipped reads + description: The index file of the output compressed text file containing the + discordant read pairs or the soft clipped reads pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi" - versions: - versions.yml: diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test new file mode 100644 index 00000000000..872352ed9a6 --- /dev/null +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process GATK4_PRINTSVEVIDENCE" + script "../main.nf" + config "./nextflow.config" + process "GATK4_PRINTSVEVIDENCE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectsvevidence" + tag "gatk4/printsvevidence" + + setup { + run("GATK4_COLLECTSVEVIDENCE") { + script "../../collectsvevidence/main.nf" + process { + """ + input[0] = Channel.of( + [ + [ id:'normal' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + [], + [] + ], + [ + [ id:'tumor' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + [], + [] + ] + ) + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + } + + test("homo sapiens - bam") { + + when { + process { + """ + files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence + indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index + input_svevidence = files + .combine(indices, by:0) + .map({ meta, file, index -> + [[id:'test'], file, index ] + }) + .groupTuple() + + input[0] = input_svevidence + input[1] = [] + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence + indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index + input_svevidence = files + .combine(indices, by:0) + .map({ meta, file, index -> + [[id:'test'], file, index ] + }) + .groupTuple() + + input[0] = input_svevidence + input[1] = [] + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap new file mode 100644 index 00000000000..74449f9ea1a --- /dev/null +++ b/modules/nf-core/gatk4/printsvevidence/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "homo sapiens - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" + ] + ], + "2": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ], + "printed_evidence": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz:md5,e466bbd14a1e511f296f8943ec60ca61" + ] + ], + "printed_evidence_index": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,e56c7481a5f4ff1a14079d9d2bb12a2d" + ] + ], + "versions": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-14T11:03:14.643404627" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ], + "printed_evidence": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "printed_evidence_index": [ + [ + { + "id": "test" + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ed39ded39eeae49d2aac81c45fb17c26" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-14T11:04:00.117599683" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/printsvevidence/tests/nextflow.config b/modules/nf-core/gatk4/printsvevidence/tests/nextflow.config new file mode 100644 index 00000000000..1d90e59c76e --- /dev/null +++ b/modules/nf-core/gatk4/printsvevidence/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_COLLECTSVEVIDENCE { + ext.args = {"--sample-name ${meta.id}"} + } +} diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 4b58bec7788..4f015396b7a 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -4,8 +4,8 @@ process GATK4_REBLOCKGVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap index 6121c3d208a..df58a6495e8 100644 --- a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap @@ -4,41 +4,41 @@ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:19.353113" + "timestamp": "2024-10-31T11:58:15.459756351" }, "test_gatk4_reblockgvcf_intervals": { "content": [ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:11.896391" + "timestamp": "2024-10-31T11:58:04.712624842" }, "test_gatk4_reblockgvcf": { "content": [ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:00.687676" + "timestamp": "2024-10-31T11:57:51.607837498" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 635784ab29f..ad2d38ab446 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -1,11 +1,11 @@ process GATK4_REVERTSAM { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap index 1cbb5ce6e79..72fda7af8e4 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:45:39.712635" + "timestamp": "2024-10-31T11:58:52.167057245" }, "test-gatk4-revertsam-stubs": { "content": [ @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ], "bam": [ [ @@ -35,14 +35,14 @@ ] ], "versions": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:45:46.856318" + "timestamp": "2024-10-31T11:59:02.762117999" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 35b9b76db4c..7760d4581bf 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -1,11 +1,11 @@ process GATK4_SAMTOFASTQ { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap index 0e1ec4b79d4..38040db0ee4 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -9,14 +9,14 @@ "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip -c > ${prefix}.baf.txt.gz + touch ${prefix}.baf.txt.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + } diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test new file mode 100644 index 00000000000..1df5fcc81e5 --- /dev/null +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test @@ -0,0 +1,116 @@ +nextflow_process { + + name "Test Process GATK4_SITEDEPTHTOBAF" + script "../main.nf" + config "./nextflow.config" + process "GATK4_SITEDEPTHTOBAF" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectsvevidence" + tag "gatk4/sitedepthtobaf" + + setup { + run("GATK4_COLLECTSVEVIDENCE") { + script "../../collectsvevidence/main.nf" + process { + """ + vcf = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true) + tbi = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) + + input[0] = Channel.of( + [ + [ id:'tumor', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + vcf, + tbi + ], + [ + [ id:'normal', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + vcf, + tbi + ] + ) + input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + } + + test("homo sapiens - bam - vcf") { + + when { + process { + """ + sitedepthtobaf_input = GATK4_COLLECTSVEVIDENCE.out.site_depths + .combine(GATK4_COLLECTSVEVIDENCE.out.site_depths_index, by:0) + .map({ meta, file, index -> [ [id:'test'], file, index ]}).groupTuple() + + input[0] = sitedepthtobaf_input + input[1] = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) + ] + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.baf[0][1]).name, + file(process.out.baf_tbi[0][1]).name + ).match() } + ) + } + + } + + test("homo sapiens - bam - vcf - stub") { + + options "-stub" + + when { + process { + """ + sitedepthtobaf_input = GATK4_COLLECTSVEVIDENCE.out.site_depths + .combine(GATK4_COLLECTSVEVIDENCE.out.site_depths_index, by:0) + .map({ meta, file, index -> [ [id:'test'], file, index ]}).groupTuple() + + input[0] = sitedepthtobaf_input + input[1] = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists: true) + ] + input[2] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.baf[0][1]).name, + file(process.out.baf_tbi[0][1]).name + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap new file mode 100644 index 00000000000..0c697cead8f --- /dev/null +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "homo sapiens - bam - vcf - stub": { + "content": [ + [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ], + "test.baf.txt.gz", + "test.baf.txt.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T07:56:28.729680029" + }, + "homo sapiens - bam - vcf": { + "content": [ + [ + "versions.yml:md5,ee6dd200adf98f0a2f1e0ab7872feb49" + ], + "test.baf.txt.gz", + "test.baf.txt.gz.tbi" + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T07:55:58.514280421" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config b/modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config new file mode 100644 index 00000000000..1d90e59c76e --- /dev/null +++ b/modules/nf-core/gatk4/sitedepthtobaf/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_COLLECTSVEVIDENCE { + ext.args = {"--sample-name ${meta.id}"} + } +} diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitcram/main.nf b/modules/nf-core/gatk4/splitcram/main.nf index 1e635cd4926..66ebd55e4e0 100644 --- a/modules/nf-core/gatk4/splitcram/main.nf +++ b/modules/nf-core/gatk4/splitcram/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITCRAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(cram) @@ -42,7 +42,6 @@ process GATK4_SPLITCRAM { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 diff --git a/modules/nf-core/gatk4/splitcram/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitcram/tests/main.nf.test.snap index 1c33e0d6e60..7801aa890fc 100644 --- a/modules/nf-core/gatk4/splitcram/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitcram/tests/main.nf.test.snap @@ -6,14 +6,14 @@ "a6cbafe874825a3dc244b4c034fb7324" ], [ - "versions.yml:md5,a979856349a9ec1ce118a89da71c9c26" + "versions.yml:md5,f97b4bbcc2e3fcec841efe3e91f7779a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-29T19:17:41.134549" + "timestamp": "2024-10-31T12:03:08.230622129" }, "test-gatk4-splitcram-stub": { "content": [ @@ -28,7 +28,7 @@ ] ], "1": [ - "versions.yml:md5,a979856349a9ec1ce118a89da71c9c26" + "versions.yml:md5,f97b4bbcc2e3fcec841efe3e91f7779a" ], "split_crams": [ [ @@ -40,14 +40,14 @@ ] ], "versions": [ - "versions.yml:md5,a979856349a9ec1ce118a89da71c9c26" + "versions.yml:md5,f97b4bbcc2e3fcec841efe3e91f7779a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-29T19:17:48.258569" + "timestamp": "2024-10-31T12:03:28.000915609" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index d59b6afb1d7..01cc5b94af3 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitintervals/meta.yml b/modules/nf-core/gatk4/splitintervals/meta.yml index 6a1b869b0d1..62dc03b0e8c 100644 --- a/modules/nf-core/gatk4/splitintervals/meta.yml +++ b/modules/nf-core/gatk4/splitintervals/meta.yml @@ -57,9 +57,18 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test' ] + pattern: "*.interval_list" - "**.interval_list": - type: file - description: interval files + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + pattern: "*.interval_list" + - s: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] pattern: "*.interval_list" - versions: - versions.yml: diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap index d055a8737d1..4eb4fa86a3b 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ] ], "1": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions.yml:md5,fc639263917642ad8064f1ff7c373684" ], "split_intervals": [ [ @@ -28,15 +28,15 @@ ] ], "versions": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions.yml:md5,fc639263917642ad8064f1ff7c373684" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:06:41.633105" + "timestamp": "2024-10-31T12:04:56.871106743" }, "test-gatk4-splitintervals-bed": { "content": [ @@ -53,7 +53,7 @@ ] ], "1": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions.yml:md5,fc639263917642ad8064f1ff7c373684" ], "split_intervals": [ [ @@ -67,15 +67,15 @@ ] ], "versions": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions.yml:md5,fc639263917642ad8064f1ff7c373684" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:06:28.504041" + "timestamp": "2024-10-31T12:04:32.783987644" }, "test-gatk4-splitintervals-intervals-stub": { "content": [ @@ -92,7 +92,7 @@ ] ], "1": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions.yml:md5,fc639263917642ad8064f1ff7c373684" ], "split_intervals": [ [ @@ -106,14 +106,14 @@ ] ], "versions": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions.yml:md5,fc639263917642ad8064f1ff7c373684" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-27T10:56:46.243594" + "timestamp": "2024-10-31T12:05:16.045688528" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index e2c287a02b1..40bfee1b30a 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -1,11 +1,11 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bai), path(intervals) @@ -46,4 +46,17 @@ process GATK4_SPLITNCIGARREADS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + } diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap index 5a3484539d9..5c2fee14781 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap @@ -3,39 +3,39 @@ "content": [ "test.bam", [ - "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:29:41.948726" + "timestamp": "2024-10-31T12:06:43.83765238" }, "test_gatk4_splitncigarreads_stub": { "content": [ "test.bam", [ - "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:29:53.2252" + "timestamp": "2024-11-07T10:35:24.483631375" }, "test_gatk4_splitncigarreads": { "content": [ "test.bam", [ - "versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb" + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:29:30.774423" + "timestamp": "2024-10-31T12:06:15.200052646" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/svannotate/main.nf b/modules/nf-core/gatk4/svannotate/main.nf index e5cf874a2b9..d81650d6ae6 100644 --- a/modules/nf-core/gatk4/svannotate/main.nf +++ b/modules/nf-core/gatk4/svannotate/main.nf @@ -4,8 +4,8 @@ process GATK4_SVANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi), path(bed) diff --git a/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap b/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap index 964713f6e1f..22e21f193b1 100644 --- a/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap @@ -4,41 +4,41 @@ "test.vcf.gz", "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", [ - "versions.yml:md5,b08053927c0e51e8282586167122f4a5" + "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:20:23.838882" + "timestamp": "2024-10-31T12:08:19.37358348" }, "test_gatk4_svannotate": { "content": [ "test.vcf.gz", "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", [ - "versions.yml:md5,b08053927c0e51e8282586167122f4a5" + "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:19:52.092072" + "timestamp": "2024-10-31T12:08:01.781002105" }, "test_gatk4_svannotate_bed": { "content": [ "test.vcf.gz", "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", [ - "versions.yml:md5,b08053927c0e51e8282586167122f4a5" + "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:20:54.131536" + "timestamp": "2024-10-31T12:08:37.914667039" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/svannotate/tests/nextflow.config b/modules/nf-core/gatk4/svannotate/tests/nextflow.config deleted file mode 100644 index 11ec85a5fc3..00000000000 --- a/modules/nf-core/gatk4/svannotate/tests/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: MANTA_GERMLINE { - enabled: false - ] - } -} diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/svcluster/main.nf b/modules/nf-core/gatk4/svcluster/main.nf index 855dd700f89..5331cd3638d 100644 --- a/modules/nf-core/gatk4/svcluster/main.nf +++ b/modules/nf-core/gatk4/svcluster/main.nf @@ -4,8 +4,8 @@ process GATK4_SVCLUSTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcfs), path(indices) diff --git a/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap b/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap index fbf5cff04c5..e49cd6ba18a 100644 --- a/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap @@ -4,13 +4,13 @@ "test.vcf.gz", "test.vcf.gz.tbi:md5,e7ca7e9fe76ce12198fd54ec9a64fad4", [ - "versions.yml:md5,9c1678d540b64d057683488a4e91a45c" + "versions.yml:md5,da1ba105c62554caf57e765b26e8fc7c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:18:12.769561" + "timestamp": "2024-10-31T12:09:27.315091" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/svcluster/tests/nextflow.config b/modules/nf-core/gatk4/svcluster/tests/nextflow.config deleted file mode 100644 index 11ec85a5fc3..00000000000 --- a/modules/nf-core/gatk4/svcluster/tests/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: MANTA_GERMLINE { - enabled: false - ] - } -} diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 388c60abf0e..5bf0e3536d3 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -1,11 +1,11 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap index 36c03f7c1e5..29cb3cdc709 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap @@ -2,29 +2,29 @@ "test_gatk4_variantfiltration_gz_input": { "content": [ [ - "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" + "versions.yml:md5,ad4241d2454ae3611dd8e7383b3109ff" ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:43:27.609784" + "timestamp": "2024-10-31T12:10:17.964554959" }, "test_gatk4_variantfiltration_vcf_input": { "content": [ [ - "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" + "versions.yml:md5,ad4241d2454ae3611dd8e7383b3109ff" ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:42:55.316294" + "timestamp": "2024-10-31T12:10:04.6172075" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 55993f440cd..1f7d0824620 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 24844ce0c95..3c6048f4ba4 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTRECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config b/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config similarity index 55% rename from tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config rename to modules/nf-core/gatk4/variantrecalibrator/tests/AS.config index 54136c7018b..eadb336e9db 100644 --- a/tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/AS.config @@ -1,9 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_COLLECTSVEVIDENCE { - ext.args = {"--sample-name ${meta.id}"} + withName: GATK4_VARIANTRECALIBRATOR { + ext.args = '-mode SNP -an QD -an MQ -an FS -AS' } - } diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test new file mode 100644 index 00000000000..2ce4b46e533 --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test @@ -0,0 +1,167 @@ +nextflow_process { + + name "Test Process GATK4_VARIANTRECALIBRATOR" + script "../main.nf" + process "GATK4_VARIANTRECALIBRATOR" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/variantrecalibrator" + + test("homo sapiens - vcf - allele specificity") { + config "./AS.config" + when { + process { + """ + input_vcf = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) + ] + + resources_vcf = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) + ] + resources_tbi = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) + ] + labels = [ + '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', + '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', + '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', + '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' + ] + + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) + + input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.recal[0][1]).name, + file(process.out.idx[0][1]).name, + process.out.tranches, + process.out.plots, + ).match() } + ) + } + + } + + test("homo sapiens - vcf - no allele specificity") { + config "./noAS.config" + when { + process { + """ + input_vcf = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) + ] + + resources_vcf = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) + ] + resources_tbi = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) + ] + labels = [ + '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', + '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', + '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', + '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' + ] + + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) + + input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.recal[0][1]).name, + file(process.out.idx[0][1]).name, + process.out.tranches, + process.out.plots, + ).match() } + ) + } + + } + + test("homo sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input_vcf = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi", checkIfExists: true) + ] + + resources_vcf = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz", checkIfExists: true) + ] + resources_tbi = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi", checkIfExists: true) + ] + labels = [ + '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', + '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', + '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', + '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' + ] + + fasta = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists: true) + fai = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true) + dict = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.dict", checkIfExists: true) + + input = [input_vcf, resources_vcf, resources_tbi, labels, fasta, fai, dict] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap new file mode 100644 index 00000000000..62882f25faa --- /dev/null +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/main.nf.test.snap @@ -0,0 +1,133 @@ +{ + "homo sapiens - vcf - allele specificity": { + "content": [ + [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ], + "test.recal", + "test.recal.idx", + [ + [ + { + "id": "test" + }, + "test.tranches:md5,ad52fa69325c758f458a30ee5b43d6b5" + ] + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:19:03.416258473" + }, + "homo sapiens - vcf - no allele specificity": { + "content": [ + [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ], + "test.recal", + "test.recal.idx", + [ + [ + { + "id": "test" + }, + "test.tranches:md5,c029e52fd63a893e1154cc9144a19eeb" + ] + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:26:53.032044124" + }, + "homo sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.recal:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.idx:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.tranches:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "testplots.R:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ], + "idx": [ + [ + { + "id": "test" + }, + "test.idx:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "plots": [ + [ + { + "id": "test" + }, + "testplots.R:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "recal": [ + [ + { + "id": "test" + }, + "test.recal:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tranches": [ + [ + { + "id": "test" + }, + "test.tranches:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,fb9c98d8bd2f8335179f7c037c63bb0d" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T10:14:43.858797367" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config b/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config similarity index 64% rename from tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config rename to modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config index e51b90449a5..69efa09ea86 100644 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config +++ b/modules/nf-core/gatk4/variantrecalibrator/tests/noAS.config @@ -5,8 +5,4 @@ process { withName: GATK4_VARIANTRECALIBRATOR { ext.args = '-mode SNP -an QD -an MQ -an FS -an SOR' } - - withName: GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY { - ext.args = '-mode SNP -an QD -an MQ -an FS -AS' - } } diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index aa7d804d4ad..d04a469c944 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -1,6 +1,11 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf index 5a189beed61..3dbb40af739 100644 --- a/modules/nf-core/gatk4/variantstotable/main.nf +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -1,14 +1,14 @@ process GATK4_VARIANTSTOTABLE { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: - tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) + tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(dict) @@ -42,8 +42,8 @@ process GATK4_VARIANTSTOTABLE { --reference $fasta \\ --tmp-dir . \\ $arguments_file_arg \\ - $include_intervals \\ - $exclude_intervals + $include_intervals_arg \\ + $exclude_intervals_arg cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap index 6560ddd65da..c6633577f63 100644 --- a/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap @@ -2,68 +2,67 @@ "test1_gatk4_variant_to_table": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.tsv:md5,fd8256465233e335beb509b0a8b43536" + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,fd8256465233e335beb509b0a8b43536" + ] + ], + "1": [ + "versions.yml:md5,b2bbb958a41e6a7ae2053052f4c4ae9f" + ], + "table": [ + [ + { + "id": "test" + }, + "test.tsv:md5,fd8256465233e335beb509b0a8b43536" + ] + ], + "versions": [ + "versions.yml:md5,b2bbb958a41e6a7ae2053052f4c4ae9f" ] - ], - "1": [ - "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" - ], - "table": [ - [ - { - "id": "test" - }, - "test.tsv:md5,fd8256465233e335beb509b0a8b43536" - ] - ], - "versions": [ - "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" - ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:43:27.609784" + "timestamp": "2024-10-31T12:11:35.809914981" }, - "test1_gatk4_variant_to_table - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" - ], - "table": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b2bbb958a41e6a7ae2053052f4c4ae9f" + ], + "table": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b2bbb958a41e6a7ae2053052f4c4ae9f" ] - ], - "versions": [ - "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" - ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:43:27.609784" + "timestamp": "2024-10-31T12:11:47.652764791" } -} +} \ No newline at end of file diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml index 14075a574ac..d3e954cdacc 100644 --- a/modules/nf-core/gatk4spark/applybqsr/environment.yml +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/applybqsr/main.nf b/modules/nf-core/gatk4spark/applybqsr/main.nf index 316ddc0b1dd..5cc5c9c4a27 100644 --- a/modules/nf-core/gatk4spark/applybqsr/main.nf +++ b/modules/nf-core/gatk4spark/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap index c4171be861f..db160a01fb6 100644 --- a/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ [ @@ -38,15 +38,15 @@ ] ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T10:12:13.226593047" + "timestamp": "2024-11-06T11:47:37.292174976" }, "sarscov2 - cram": { "content": [ @@ -63,7 +63,7 @@ ] ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ @@ -77,15 +77,15 @@ ] ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:43:27.971279286" + "timestamp": "2024-11-06T11:48:24.575560544" }, "sarscov2 - bam": { "content": [ @@ -102,7 +102,7 @@ ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ [ @@ -116,15 +116,15 @@ ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:40:33.915518205" + "timestamp": "2024-11-06T11:46:46.042894548" }, "sarscov2 - bam intervals": { "content": [ @@ -141,7 +141,7 @@ ], "2": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ], "bam": [ [ @@ -155,14 +155,14 @@ ], "versions": [ - "versions.yml:md5,908022a782ee4e7d9c8264a2aa2c1c9f" + "versions.yml:md5,985dcafacddb7013ec01b73fd9163290" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:42:52.310003463" + "timestamp": "2024-11-06T11:47:13.436442722" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml index 14075a574ac..d3e954cdacc 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/modules/nf-core/gatk4spark/baserecalibrator/main.nf index 32af761912f..304b1bc5240 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4spark/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) @@ -51,4 +51,16 @@ process GATK4SPARK_BASERECALIBRATOR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.table + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test new file mode 100644 index 00000000000..ff6867d2f24 --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test @@ -0,0 +1,160 @@ +nextflow_process { + + name "Test Process GATK4SPARK_BASERECALIBRATOR" + script "../main.nf" + config "./nextflow.config" + process "GATK4SPARK_BASERECALIBRATOR" + + tag "modules" + tag "modules_nfcore" + tag "gatk4spark" + tag "gatk4spark/baserecalibrator" + + test("sarscov2 - bam") { + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo sapiens - cram") { + when { + process { + """ + input_cram = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + + input = [input_cram, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - intervals") { + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - multi sites") { + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)] + sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)] + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input_bam = [ [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + input = [input_bam, fasta, fai, dict, sites, sites_tbi] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap new file mode 100644 index 00000000000..c02ce4b1c8e --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test.snap @@ -0,0 +1,167 @@ +{ + "sarscov2 - bam - multi sites": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:52:50.311106222" + }, + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:38:35.054385124" + }, + "homo sapiens - cram": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,ab82f81e027d8762b01c631b4ef792c0" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,ab82f81e027d8762b01c631b4ef792c0" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T12:03:12.23567219" + }, + "sarscov2 - bam - intervals": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:51:34.077518575" + }, + "sarscov2 - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "1": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "versions": [ + "versions.yml:md5,d98a4e7d4b5c7b7c59268214c538bd58" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T11:49:36.893419883" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config b/modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config new file mode 100644 index 00000000000..a1a17be887d --- /dev/null +++ b/modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config @@ -0,0 +1,2 @@ +docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' + diff --git a/modules/nf-core/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml index 14075a574ac..d3e954cdacc 100644 --- a/modules/nf-core/gatk4spark/markduplicates/environment.yml +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4-spark=4.5.0.0 + - bioconda::gatk4-spark=4.6.1.0 diff --git a/modules/nf-core/gatk4spark/markduplicates/main.nf b/modules/nf-core/gatk4spark/markduplicates/main.nf index b6a6daffea4..9cb74c8b363 100644 --- a/modules/nf-core/gatk4spark/markduplicates/main.nf +++ b/modules/nf-core/gatk4spark/markduplicates/main.nf @@ -4,8 +4,8 @@ process GATK4SPARK_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.5.0.0--hdfd78af_0': - 'biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4-spark:4.6.1.0--hdfd78af_0': + 'biocontainers/gatk4-spark:4.6.1.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap index 4968a1ce650..f9366caead2 100644 --- a/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test.snap @@ -24,7 +24,7 @@ ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ [ @@ -48,15 +48,15 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:53:11.621016088" + "timestamp": "2024-11-06T11:52:48.84070018" }, "homo_sapiens - bam - metrics - output": { "content": [ @@ -95,7 +95,7 @@ ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ @@ -113,27 +113,27 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:53:53.339811107" + "timestamp": "2024-11-06T11:54:09.554533288" }, "homo_sapiens - bam - metrics - versions": { "content": [ [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:53:32.199010065" + "timestamp": "2024-11-06T11:53:39.648663125" }, "homo_sapiens - bam - metrics - bam_index": { "content": [ @@ -184,7 +184,7 @@ ] ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ [ @@ -214,15 +214,15 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T10:56:48.15652292" + "timestamp": "2024-11-06T11:54:21.987287007" }, "sarscov2 - bam": { "content": [ @@ -249,7 +249,7 @@ ], "3": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ], "bam_index": [ [ @@ -273,14 +273,14 @@ ] ], "versions": [ - "versions.yml:md5,9699197d0e667ab368a8c6d2a6893cc6" + "versions.yml:md5,1184eb9fbc4a9cb7384b760b2c112c94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T11:52:51.5386181" + "timestamp": "2024-11-06T11:51:28.270175346" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 8a781b0c78c..c770ce2a61e 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -191,45 +191,9 @@ gangstr: gatk/indelrealigner: - modules/nf-core/gatk/indelrealigner/** - tests/modules/nf-core/gatk/indelrealigner/** -gatk4/cnnscorevariants: - - modules/nf-core/gatk4/cnnscorevariants/** - - tests/modules/nf-core/gatk4/cnnscorevariants/** -gatk4/createreadcountpanelofnormals: - - modules/nf-core/gatk4/createreadcountpanelofnormals/** - - tests/modules/nf-core/gatk4/createreadcountpanelofnormals/** -gatk4/createsomaticpanelofnormals: - - modules/nf-core/gatk4/createsomaticpanelofnormals/** - - tests/modules/nf-core/gatk4/createsomaticpanelofnormals/** -gatk4/determinegermlinecontigploidy: - - modules/nf-core/gatk4/determinegermlinecontigploidy/** - - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/** -gatk4/filtervarianttranches: - - modules/nf-core/gatk4/filtervarianttranches/** - - tests/modules/nf-core/gatk4/filtervarianttranches/** -gatk4/germlinecnvcaller: - - modules/nf-core/gatk4/germlinecnvcaller/** - - tests/modules/nf-core/gatk4/germlinecnvcaller/** -gatk4/intervallisttobed: - - modules/nf-core/gatk4/intervallisttobed/** - - tests/modules/nf-core/gatk4/intervallisttobed/** -gatk4/postprocessgermlinecnvcalls: - - modules/nf-core/gatk4/postprocessgermlinecnvcalls/** - - tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/** -gatk4/printsvevidence: - - modules/nf-core/gatk4/printsvevidence/** - - tests/modules/nf-core/gatk4/printsvevidence/** gatk4/selectsamples: - modules/nf-core/gatk4/selectsamples/** - tests/modules/nf-core/gatk4/selectsamples/** -gatk4/sitedepthtobaf: - - modules/nf-core/gatk4/sitedepthtobaf/** - - tests/modules/nf-core/gatk4/sitedepthtobaf/** -gatk4/variantrecalibrator: - - modules/nf-core/gatk4/variantrecalibrator/** - - tests/modules/nf-core/gatk4/variantrecalibrator/** -gatk4spark/baserecalibrator: - - modules/nf-core/gatk4spark/baserecalibrator/** - - tests/modules/nf-core/gatk4spark/baserecalibrator/** gem2/gem2bedmappability: - modules/nf-core/gem2/gem2bedmappability/** - tests/modules/nf-core/gem2/gem2bedmappability/** diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf b/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf deleted file mode 100644 index 8a218e1b884..00000000000 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' - -workflow test_gatk4_cnnscorevariants { - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - [], - [] - ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] ) -} diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config b/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml b/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml deleted file mode 100644 index c26b9eab72d..00000000000 --- a/tests/modules/nf-core/gatk4/cnnscorevariants/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants - command: nextflow run ./tests/modules/nf-core/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/cnnscorevariants/nextflow.config - tags: - - gatk4/cnnscorevariants - - gatk4 - files: - - path: output/gatk4/test.cnn.vcf.gz - contains: ["##ALT= list} - .set {ch_intervals} - - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - ]).combine(ch_intervals) - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - GATK4_CREATEREADCOUNTPANELOFNORMALS ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - ) -} diff --git a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml b/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml deleted file mode 100644 index 829079feaa5..00000000000 --- a/tests/modules/nf-core/gatk4/createreadcountpanelofnormals/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: "gatk4 createreadcountpanelofnormals" - command: nextflow run ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals -entry test_gatk4_createreadcountpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config - tags: - - "gatk4" - - "gatk4/createreadcountpanelofnormals" - files: - - path: "output/gatk4/test.hdf5" - - path: "output/gatk4/versions.yml" - -- name: "gatk4 createreadcountpanelofnormals stub" - command: nextflow run ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals -entry test_gatk4_createreadcountpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createreadcountpanelofnormals/nextflow.config -stub - tags: - - "gatk4" - - "gatk4/createreadcountpanelofnormals" - files: - - path: "output/gatk4/test.hdf5" - - path: "output/gatk4/versions.yml" diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf deleted file mode 100644 index bd626961f69..00000000000 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf' -include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf' - -workflow test_gatk4_createsomaticpanelofnormals { - db = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ] - - UNTAR ( db ) - - input = Channel.of([ id:'test']) - .combine(UNTAR.out.untar.map{ it[1] }) - - fasta = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - dict = [ [ id:'genome' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - ] - - GATK4_CREATESOMATICPANELOFNORMALS ( input, fasta, fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config deleted file mode 100644 index 0db1ebba6c2..00000000000 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config +++ /dev/null @@ -1,13 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_CREATESOMATICPANELOFNORMALS { - ext.prefix = { "${meta.id}.pon" } - } - - withName: UNTAR { - publishDir = [ enabled: false ] - } - -} diff --git a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml b/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml deleted file mode 100644 index a2a9fc182ae..00000000000 --- a/tests/modules/nf-core/gatk4/createsomaticpanelofnormals/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: gatk4 createsomaticpanelofnormals test_gatk4_createsomaticpanelofnormals - command: nextflow run ./tests/modules/nf-core/gatk4/createsomaticpanelofnormals -entry test_gatk4_createsomaticpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/createsomaticpanelofnormals/nextflow.config - tags: - - gatk4/createsomaticpanelofnormals - - gatk4 - files: - - path: output/gatk4/test.pon.vcf.gz - - path: output/gatk4/test.pon.vcf.gz.tbi - md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf deleted file mode 100644 index 508a4d3caf0..00000000000 --- a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_CASE } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' - -workflow test_gatk4_determinegermlinecontigploidy { - - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ]) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), - [[],[]], - contig_ploidy_table - ) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_CASE ( - GATK4_COLLECTREADCOUNTS.out.tsv - .first() - .map({ meta, tsv -> [ [id:'test_case'], tsv, [], [] ] }), - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.model, - [] - ) -} - -workflow test_gatk4_determinegermlinecontigploidy_cohort_exclude_intervals { - - bed_1 = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) - .map({bed -> return bed.text.replace("40001","10001") + "chr22\t10001\t40001\n" }) - .collectFile( name: "genome.bed" ) - - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) - ]).combine(bed_1) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - bed_2 = Channel.of(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) - .map({bed -> return bed.text.replaceFirst("0","10001") }) - .collectFile( name: "genome_exclude.bed" ) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed_2) - .map({ meta, counts, bed -> [ meta, counts, [], bed ]}), - [[],[]], - contig_ploidy_table - ) -} diff --git a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml b/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml deleted file mode 100644 index 5f42e6e43cf..00000000000 --- a/tests/modules/nf-core/gatk4/determinegermlinecontigploidy/test.yml +++ /dev/null @@ -1,31 +0,0 @@ -- name: gatk4 determinegermlinecontigploidy test_gatk4_determinegermlinecontigploidy - command: nextflow run ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy -entry test_gatk4_determinegermlinecontigploidy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config - tags: - - gatk4/determinegermlinecontigploidy - - gatk4 - files: - - path: output/gatk4/test-calls - - path: output/gatk4/test-model - - path: output/gatk4/test_case-calls - - path: output/gatk4/versions.yml - -- name: gatk4 determinegermlinecontigploidy test_gatk4_determinegermlinecontigploidy_cohort_exclude_intervals - command: nextflow run ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy -entry test_gatk4_determinegermlinecontigploidy_cohort_exclude_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config - tags: - - gatk4/determinegermlinecontigploidy - - gatk4 - files: - - path: output/gatk4/test-calls - - path: output/gatk4/test-model - - path: output/gatk4/versions.yml - -- name: gatk4 determinegermlinecontigploidy test_gatk4_determinegermlinecontigploidy_stub - command: nextflow run ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy -entry test_gatk4_determinegermlinecontigploidy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/determinegermlinecontigploidy/nextflow.config -stub - tags: - - gatk4/determinegermlinecontigploidy - - gatk4 - files: - - path: output/gatk4/test-calls - - path: output/gatk4/test-model - - path: output/gatk4/test_case-calls - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf b/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf deleted file mode 100644 index 5b2b0d484b3..00000000000 --- a/tests/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_FILTERVARIANTTRANCHES } from '../../../../../modules/nf-core/gatk4/filtervarianttranches/main.nf' -include { GATK4_CNNSCOREVARIANTS } from '../../../../../modules/nf-core/gatk4/cnnscorevariants/main.nf' -include { GATK4_HAPLOTYPECALLER } from '../../../../../modules/nf-core/gatk4/haplotypecaller/main.nf' -workflow test_gatk4_filtervarianttranches { - - resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - resources_index = [ - file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true), - ] - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), - [] - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - GATK4_FILTERVARIANTTRANCHES (input , resources, resources_index, fasta, fai, dict) -} diff --git a/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml b/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml deleted file mode 100644 index 23a782d05ef..00000000000 --- a/tests/modules/nf-core/gatk4/filtervarianttranches/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gatk4 filtervarianttranches test_gatk4_filtervarianttranches - command: nextflow run ./tests/modules/nf-core/gatk4/filtervarianttranches -entry test_gatk4_filtervarianttranches -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filtervarianttranches/nextflow.config - tags: - - gatk4/filtervarianttranches - - gatk4 - files: - - path: output/gatk4/test.filtered.vcf.gz - - path: output/gatk4/test.filtered.vcf.gz.tbi - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf deleted file mode 100644 index 1908a1cb32d..00000000000 --- a/tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_GERMLINECNVCALLER as GATK4_GERMLINECNVCALLER_COHORT } from '../../../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' -include { GATK4_GERMLINECNVCALLER as GATK4_GERMLINECNVCALLER_CASE } from '../../../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' - -workflow test_gatk4_germlinecnvcaller { - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ]) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), - [[],[]], - contig_ploidy_table - ) - - intervals = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ] - GATK4_BEDTOINTERVALLIST ( intervals, dict ) - - gcnvc_cohort_input = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ]}) - .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) - .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} - - GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input ) - - gcnvc_case_input = GATK4_COLLECTREADCOUNTS.out.tsv.first() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .map{ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]} - GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input ) - -} diff --git a/tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config b/tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config deleted file mode 100644 index 88f61a49e11..00000000000 --- a/tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config +++ /dev/null @@ -1,21 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'GATK4_COLLECTREADCOUNTS*' { - ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" - } - - withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT' { - ext.args = "--interval-merging-rule OVERLAPPING_ONLY" - } - - withName: 'GATK4_GERMLINECNVCALLER_COHORT' { - ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" - } - - withName: 'GATK4_GERMLINECNVCALLER_CASE' { - ext.args = "--run-mode CASE" - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml b/tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml deleted file mode 100644 index f78fbfafb86..00000000000 --- a/tests/modules/nf-core/gatk4/germlinecnvcaller/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: gatk4 germlinecnvcaller test_gatk4_germlinecnvcaller - command: nextflow run ./tests/modules/nf-core/gatk4/germlinecnvcaller -entry test_gatk4_germlinecnvcaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config - tags: - - gatk4/germlinecnvcaller - - gatk4 - files: - - path: output/gatk4/test-cnv-model/test-model - - path: output/gatk4/test-cnv-model/test-calls - - path: output/gatk4/test-cnv-calls/test-calls - - path: output/gatk4/versions.yml - -- name: gatk4 germlinecnvcaller test_gatk4_germlinecnvcaller_stub - command: nextflow run ./tests/modules/nf-core/gatk4/germlinecnvcaller -entry test_gatk4_germlinecnvcaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/germlinecnvcaller/nextflow.config -stub - tags: - - gatk4/germlinecnvcaller - - gatk4 - files: - - path: output/gatk4/test-cnv-model/test-model - - path: output/gatk4/test-cnv-model/test-calls - - path: output/gatk4/test-cnv-calls/test-calls - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf b/tests/modules/nf-core/gatk4/intervallisttobed/main.nf deleted file mode 100644 index c8a5b819098..00000000000 --- a/tests/modules/nf-core/gatk4/intervallisttobed/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_INTERVALLISTTOBED } from '../../../../../modules/nf-core/gatk4/intervallisttobed/main.nf' - -workflow test_gatk4_intervallisttobed { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) - ] - - GATK4_INTERVALLISTTOBED ( input ) -} diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config b/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/gatk4/intervallisttobed/test.yml b/tests/modules/nf-core/gatk4/intervallisttobed/test.yml deleted file mode 100644 index 461d484c855..00000000000 --- a/tests/modules/nf-core/gatk4/intervallisttobed/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gatk4 intervallisttobed - command: nextflow run ./tests/modules/nf-core/gatk4/intervallisttobed -entry test_gatk4_intervallisttobed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/intervallisttobed/nextflow.config - tags: - - gatk4 - - gatk4/intervallisttobed - files: - - path: output/gatk4/test.bed - md5sum: 9046675d01199fbbee79f2bc1c5dce52 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf deleted file mode 100644 index e6314d6c045..00000000000 --- a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ /dev/null @@ -1,85 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf' -include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf' -include { GATK4_DETERMINEGERMLINECONTIGPLOIDY as GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT } from '../../../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' -include { GATK4_GERMLINECNVCALLER as GATK4_GERMLINECNVCALLER_COHORT } from '../../../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' -include { GATK4_GERMLINECNVCALLER as GATK4_GERMLINECNVCALLER_CASE } from '../../../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' -include { GATK4_POSTPROCESSGERMLINECNVCALLS as GATK4_POSTPROCESSGERMLINECNVCALLS_COHORT } from '../../../../../modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf' -include { GATK4_POSTPROCESSGERMLINECNVCALLS as GATK4_POSTPROCESSGERMLINECNVCALLS_CASE } from '../../../../../modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf' - -workflow test_gatk4_postprocessgermlinecnvcalls { - input = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ]) - - fasta = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]).collect() - - GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict ) - - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)) - contig_ploidy_table = file(params.test_data['homo_sapiens']['illumina']['contig_ploidy_priors_table'], checkIfExists: true) - - GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT ( - GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ] }) - .groupTuple() - .combine(bed) - .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), - [[],[]], - contig_ploidy_table - ) - -// - intervals = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) - ] - GATK4_BEDTOINTERVALLIST ( intervals, dict ) -// - gcnvc_cohort_input = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [ [id:'test'], tsv ]}) - .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) - .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) - - GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input ) - - gcnvc_case_input = GATK4_COLLECTREADCOUNTS.out.tsv - .first() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) - GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input ) - - GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [ [id:'test'], calls, model, ploidy ]}) - .set {postproc_in_cohort} - - GATK4_POSTPROCESSGERMLINECNVCALLS_COHORT ( postproc_in_cohort ) - - GATK4_GERMLINECNVCALLER_CASE.out.casecalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [ [id:'test'], calls, model, ploidy ]}) - .set {postproc_in_calls} - - GATK4_POSTPROCESSGERMLINECNVCALLS_CASE ( postproc_in_calls ) - -} diff --git a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml b/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml deleted file mode 100644 index 8ffb86ad0f9..00000000000 --- a/tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: gatk4 postprocessgermlinecnvcalls test_gatk4_postprocessgermlinecnvcalls - command: nextflow run ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls -entry test_gatk4_postprocessgermlinecnvcalls -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config - tags: - - gatk4/postprocessgermlinecnvcalls - - gatk4 - files: - - path: output/gatk4/test_denoised.vcf.gz - - path: output/gatk4/test_genotyped_intervals.vcf.gz - - path: output/gatk4/test_genotyped_segments.vcf.gz - - path: output/gatk4/versions.yml - -- name: gatk4 postprocessgermlinecnvcalls test_gatk4_postprocessgermlinecnvcalls stub - command: nextflow run ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls -entry test_gatk4_postprocessgermlinecnvcalls -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/nextflow.config -stub - tags: - - gatk4/postprocessgermlinecnvcalls - - gatk4 - files: - - path: output/gatk4/test_denoised.vcf.gz - - path: output/gatk4/test_genotyped_intervals.vcf.gz - - path: output/gatk4/test_genotyped_segments.vcf.gz - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/printsvevidence/main.nf b/tests/modules/nf-core/gatk4/printsvevidence/main.nf deleted file mode 100644 index 16309838a94..00000000000 --- a/tests/modules/nf-core/gatk4/printsvevidence/main.nf +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_PRINTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/printsvevidence/main.nf' -include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' - -workflow test_gatk4_printsvevidence { - - input = Channel.of( - [ - [ id:'normal' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ], - [ - [ id:'tumor' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ] - ) - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - - GATK4_COLLECTSVEVIDENCE( - input, - fasta, - fasta_fai, - dict - ) - - files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence - - indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index - - input_svevidence = files.combine(indices, by:0).map({ meta, file, index -> - [ [id:'pe_files'], file, index ] - }) - .groupTuple() - - GATK4_PRINTSVEVIDENCE( - input_svevidence, - [], - fasta, - fasta_fai, - dict - ) -} - -workflow test_gatk4_printsvevidence_bed_no_fasta { - - input = Channel.of( - [ - [ id:'normal', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ], - [ - [ id:'tumor', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - [], - [] - ] - ) - - fasta = [] - fasta_fai = [] - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) - - GATK4_COLLECTSVEVIDENCE( - input, - fasta, - fasta_fai, - dict - ) - - files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence - - indices = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index - - input_svevidence = files.combine(indices, by:0).map({ meta, file, index -> - [ [id:'pe_files'], file, index ] - }) - .groupTuple() - - GATK4_PRINTSVEVIDENCE( - input_svevidence, - [], - fasta, - fasta_fai, - dict - ) - -} diff --git a/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config b/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config deleted file mode 100644 index 54136c7018b..00000000000 --- a/tests/modules/nf-core/gatk4/printsvevidence/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GATK4_COLLECTSVEVIDENCE { - ext.args = {"--sample-name ${meta.id}"} - } - -} diff --git a/tests/modules/nf-core/gatk4/printsvevidence/test.yml b/tests/modules/nf-core/gatk4/printsvevidence/test.yml deleted file mode 100644 index 26f16234a97..00000000000 --- a/tests/modules/nf-core/gatk4/printsvevidence/test.yml +++ /dev/null @@ -1,55 +0,0 @@ -- name: gatk4 printsvevidence test_gatk4_printsvevidence - command: nextflow run ./tests/modules/nf-core/gatk4/printsvevidence -entry test_gatk4_printsvevidence -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printsvevidence/nextflow.config - tags: - - gatk4/printsvevidence - - gatk4 - files: - - path: output/gatk4/normal.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/normal.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/normal.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/normal.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/pe_files.pe.txt.gz - md5sum: 01af37919a5df7353096789fe526a33f - - path: output/gatk4/pe_files.pe.txt.gz.tbi - md5sum: e56c7481a5f4ff1a14079d9d2bb12a2d - - path: output/gatk4/tumor.pe.txt.gz - md5sum: 45be73eb7d52e901b6dd8a5e48bf2161 - - path: output/gatk4/tumor.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/tumor.sr.txt.gz - md5sum: afdf79e9b07035df28d6c8313661931b - - path: output/gatk4/tumor.sr.txt.gz.tbi - md5sum: 8207e46090fdbe125ce6936ac383da40 - - path: output/gatk4/versions.yml - -- name: gatk4 printsvevidence test_gatk4_printsvevidence_bed_no_fasta - command: nextflow run ./tests/modules/nf-core/gatk4/printsvevidence -entry test_gatk4_printsvevidence_bed_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printsvevidence/nextflow.config - tags: - - gatk4/printsvevidence - - gatk4 - files: - - path: output/gatk4/normal.pe.txt.gz - md5sum: 19f13dd0408204590b40239d14acbdde - - path: output/gatk4/normal.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/normal.sr.txt.gz - md5sum: fb9ce52193a0db3a084890bd6bbf6a64 - - path: output/gatk4/normal.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/pe_files.pe.txt.gz - md5sum: 01af37919a5df7353096789fe526a33f - - path: output/gatk4/pe_files.pe.txt.gz.tbi - md5sum: e56c7481a5f4ff1a14079d9d2bb12a2d - - path: output/gatk4/tumor.pe.txt.gz - md5sum: 45be73eb7d52e901b6dd8a5e48bf2161 - - path: output/gatk4/tumor.pe.txt.gz.tbi - md5sum: a41bb7768ba058a95c67b69bad9e096d - - path: output/gatk4/tumor.sr.txt.gz - md5sum: afdf79e9b07035df28d6c8313661931b - - path: output/gatk4/tumor.sr.txt.gz.tbi - md5sum: 8207e46090fdbe125ce6936ac383da40 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf b/tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf deleted file mode 100644 index 734e2ccde01..00000000000 --- a/tests/modules/nf-core/gatk4/sitedepthtobaf/main.nf +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_SITEDEPTHTOBAF } from '../../../../../modules/nf-core/gatk4/sitedepthtobaf/main.nf' -include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf' - -workflow test_gatk4_sitedepthtobaf { - - vcf = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true) - tbi = file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) - - input = Channel.of([ - [ id:'tumor', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - vcf, - tbi - ], - [ - [ id:'normal', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), - vcf, - tbi - ] - ) - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - - GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict ) - - sitedepthtobaf_input = GATK4_COLLECTSVEVIDENCE.out.site_depths - .combine(GATK4_COLLECTSVEVIDENCE.out.site_depths_index, by:0) - .map({ meta, file, index -> [ [id:'test'], file, index ]}).groupTuple() - - GATK4_SITEDEPTHTOBAF ( sitedepthtobaf_input, [ vcf, tbi ], fasta, fasta_fai, dict ) -} diff --git a/tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml b/tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml deleted file mode 100644 index 16ce5b445fc..00000000000 --- a/tests/modules/nf-core/gatk4/sitedepthtobaf/test.yml +++ /dev/null @@ -1,35 +0,0 @@ -- name: gatk4 sitedepthtobaf test_gatk4_sitedepthtobaf - command: nextflow run ./tests/modules/nf-core/gatk4/sitedepthtobaf -entry test_gatk4_sitedepthtobaf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/sitedepthtobaf/nextflow.config - tags: - - gatk4/sitedepthtobaf - - gatk4 - files: - - path: output/gatk4/normal.pe.txt.gz - md5sum: aa7489b9024c8ac39c39a5f020b98d1c - - path: output/gatk4/normal.pe.txt.gz.tbi - md5sum: 99324af842f3236a1e78703d06992648 - - path: output/gatk4/normal.sd.txt.gz - md5sum: b83b89a84e35a0b071ce2bbba84c7ca7 - - path: output/gatk4/normal.sd.txt.gz.tbi - md5sum: bff6f3811b84019316ee8e5b6c9ab9bb - - path: output/gatk4/normal.sr.txt.gz - md5sum: 2881e2e9fa1b9b6c02f0a756e25ff96a - - path: output/gatk4/normal.sr.txt.gz.tbi - md5sum: 8207e46090fdbe125ce6936ac383da40 - - path: output/gatk4/test.baf.txt.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: output/gatk4/test.baf.txt.gz.tbi - md5sum: 2f146ddadfd39ca5f1f2fd79f727d427 - - path: output/gatk4/tumor.pe.txt.gz - md5sum: 566a9621ff7ee1d12e7593d953db5344 - - path: output/gatk4/tumor.pe.txt.gz.tbi - md5sum: 513329f5ba4b6c982f03beea47a8ba53 - - path: output/gatk4/tumor.sd.txt.gz - md5sum: bd90f752f403f054abf64bddf4433f6c - - path: output/gatk4/tumor.sd.txt.gz.tbi - md5sum: 4a4dba7c9060ac0206f123d0ab2cb733 - - path: output/gatk4/tumor.sr.txt.gz - md5sum: b95035ddc709ed6602624459600c4d47 - - path: output/gatk4/tumor.sr.txt.gz.tbi - md5sum: 33b3a9ff444eb0e0fc3016239651f05f - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf b/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf deleted file mode 100644 index f8680f9dec1..00000000000 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ /dev/null @@ -1,72 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' -include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../../modules/nf-core/gatk4/variantrecalibrator/main.nf' - -workflow test_gatk4_variantrecalibrator { - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) - ] - - resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) - ] - resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) - ] - labels = [ - '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', - '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', - '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', - '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - - GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict) -} - -workflow test_gatk4_variantrecalibrator_allele_specific { - - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true) - ] - - resources_vcf = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) - ] - resources_tbi = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) - ] - labels = [ - '--resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', - '--resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', - '--resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', - '--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - - GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY(input, resources_vcf, resources_tbi, labels, fasta, fai, dict) -} diff --git a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml b/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml deleted file mode 100644 index b24b45cbe13..00000000000 --- a/tests/modules/nf-core/gatk4/variantrecalibrator/test.yml +++ /dev/null @@ -1,27 +0,0 @@ -- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator - command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config - tags: - - gatk4 - - gatk4/variantrecalibrator - files: - - path: output/gatk4/test.recal - contains: - - "#CHROM POS ID REF ALT QUAL FILTER INFO" - - path: output/gatk4/test.recal.idx - - path: output/gatk4/test.tranches - md5sum: c029e52fd63a893e1154cc9144a19eeb - - path: output/gatk4/versions.yml - -- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific - command: nextflow run ./tests/modules/nf-core/gatk4/variantrecalibrator -entry test_gatk4_variantrecalibrator_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/variantrecalibrator/nextflow.config - tags: - - gatk4 - - gatk4/variantrecalibrator - files: - - path: output/gatk4/test.recal - contains: - - "#CHROM POS ID REF ALT QUAL FILTER INFO" - - path: output/gatk4/test.recal.idx - - path: output/gatk4/test.tranches - md5sum: ad52fa69325c758f458a30ee5b43d6b5 - - path: output/gatk4/versions.yml diff --git a/tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf b/tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf deleted file mode 100644 index 79d5bbeeea2..00000000000 --- a/tests/modules/nf-core/gatk4spark/baserecalibrator/main.nf +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4SPARK_BASERECALIBRATOR } from '../../../../../modules/nf-core/gatk4spark/baserecalibrator/main.nf' - -workflow test_gatk4spark_baserecalibrator { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [] - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} - -workflow test_gatk4spark_baserecalibrator_cram { - input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - [] - ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} - -workflow test_gatk4spark_baserecalibrator_intervals { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} - -workflow test_gatk4spark_baserecalibrator_multiple_sites { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - [] - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - sites = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - ] - sites_tbi = [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - ] - - GATK4SPARK_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi ) -} diff --git a/tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config b/tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml b/tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml deleted file mode 100644 index 61bebf2725d..00000000000 --- a/tests/modules/nf-core/gatk4spark/baserecalibrator/test.yml +++ /dev/null @@ -1,39 +0,0 @@ -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: e2e43abdc0c943c1a54dae816d0b9ea7 - - path: output/gatk4spark/versions.yml - -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator_cram - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: 35d89a3811aa31711fc9815b6b80e6ec - - path: output/gatk4spark/versions.yml - -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator_intervals - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: 9ecb5f00a2229291705addc09c0ec231 - - path: output/gatk4spark/versions.yml - -- name: gatk4spark baserecalibrator test_gatk4spark_baserecalibrator_multiple_sites - command: nextflow run ./tests/modules/nf-core/gatk4spark/baserecalibrator -entry test_gatk4spark_baserecalibrator_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4spark/baserecalibrator/nextflow.config - tags: - - gatk4spark - - gatk4spark/baserecalibrator - files: - - path: output/gatk4spark/test.table - md5sum: e2e43abdc0c943c1a54dae816d0b9ea7 - - path: output/gatk4spark/versions.yml