Merge branch 'master' into umitools_nftest

nf-core · Nov 20, 2024 · 10ea39a · 10ea39a
2 parents a3a97ba + ba85edc
commit 10ea39a
Show file tree

Hide file tree

Showing 257 changed files with 3,645 additions and 2,025 deletions.
diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -35,7 +35,7 @@ runs:
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
       with:
-        version: "${{ env.NFTEST_VERSION }}"
+        version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer

diff --git a/.github/renovate.json5 b/.github/renovate.json5
@@ -23,7 +23,7 @@
                     "(^|/)action\\.ya?ml$"
                 ],
                 "matchStrings": [
-                    "# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
+                    "# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VER(SION)?\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
                 ]
             }
         ]

diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -30,27 +30,59 @@ concurrency:
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
-  NFTEST_VERSION: "0.9.2"
+  NFT_VER: "0.9.2"
   NXF_ANSI_LOG: false
   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:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose detected tags as 'modules' and 'workflows' output variables
+      paths: ${{ steps.list.outputs.components }}
+      modules: ${{ steps.outputs.outputs.modules }}
+      subworkflows: ${{ steps.outputs.outputs.subworkflows}}
+      # Prod for version bumping
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@e114e734c3bfa4599151087dcbc457ff38e5bf2c
+        with:
+          head: ${{ github.sha }}
+          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
+          n_parents: 2
+          tags: "gpu"
+
+      - name: Separate modules and subworkflows
+        id: outputs
+        run: |
+          echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT
+          echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT
+      - name: debug
+        run: |
+          echo ${{ steps.filter.outputs.components }}
+          echo ${{ steps.outputs.outputs.modules }}
+          echo ${{ steps.outputs.outputs.subworkflows }}
+
   nf-test-gpu:
     runs-on: "gpu"
+    needs: nf-test-changes
+    if: ${{ fromJSON(needs.nf-test-changes.outputs.paths) != '[]' || needs.nf-test-changes.outputs.paths != '' }}
     name: "GPU | ${{ matrix.tags}} | ${{ matrix.profile }} | ${{ matrix.shard }}"
     strategy:
       fail-fast: false
       matrix:
         shard: [1, 2]
         profile: [docker_self_hosted, singularity] # conda?
-        # TODO Pass these in from GitHub PR trigger events
-        tags:
-          - parabricks/applybqsr
-          - parabricks/fq2bam
-          - parabricks/fq2bammeth
+        tags: ${{ fromJSON(needs.nf-test-changes.outputs.modules) && fromJSON(needs.nf-test-changes.outputs.subworkflows) }}
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: 2

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -27,12 +27,12 @@ concurrency:
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
-  NFTEST_VERSION: "0.9.2"
+  NFT_VER: "0.9.2"
   NXF_ANSI_LOG: false
   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
@@ -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
@@ -13,9 +13,9 @@ env:
   # renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
   WAVE_VERSION: "1.5.0"
   # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
-  NFTEST_VERSION: "0.9.1"
+  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:
@@ -143,7 +143,7 @@ jobs:
 
   #     - uses: nf-core/setup-nf-test@v1
   #       with:
-  #         version: ${{ env.NFTEST_VERSION }}
+  #         version: ${{ env.NFT_VER }}
 
   #     - name: Bump Snapshot Versions
   #       env:

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"
     }
 }