Merge branch 'master' into umi_handling

nf-core · Dec 12, 2024 · 7288959 · 7288959
2 parents e620501 + 9a19690
commit 7288959
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Showing 133 changed files with 4,230 additions and 1,490 deletions.
diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
@@ -182,3 +182,11 @@ exclude:
     path: modules/nf-core/xeniumranger/resegment
   - profile: conda
     path: modules/nf-core/xeniumranger/import-segmentation
+  - profile: conda
+    path: modules/nf-core/parabricks/dbsnp
+  - profile: conda
+    path: modules/nf-core/parabricks/indexgvcf
+  - profile: conda
+    path: modules/nf-core/parabricks/genotypegvcf
+  - profile: conda
+    path: modules/nf-core/parabricks/applybqsr
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -108,13 +108,18 @@ jobs:
     needs: [nf-test-gpu]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -109,7 +109,7 @@ jobs:
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+      - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
         id: cache-pip
         with:
           path: ~/.cache/pip

diff --git 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_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -110,13 +110,18 @@ jobs:
     needs: [nf-test]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -247,7 +247,7 @@ jobs:
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+      - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
         id: cache-pip-pytest
         with:
           path: ~/.cache/pip

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
@@ -31,7 +31,7 @@ jobs:
 
       - name: Find conda differences
         id: conda-diff
-        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
+        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
         with:
           json: true
           escape_json: false
@@ -40,7 +40,7 @@ jobs:
 
       - name: Find Dockerfile differences
         id: docker-diff
-        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
+        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
         with:
           json: true
           escape_json: false

diff --git a/modules/nf-core/ampcombi2/cluster/environment.yml b/modules/nf-core/ampcombi2/cluster/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"
diff --git a/modules/nf-core/ampcombi2/cluster/main.nf b/modules/nf-core/ampcombi2/cluster/main.nf
@@ -4,8 +4,8 @@ process AMPCOMBI2_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     path(summary_file)

diff --git a/modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap b/modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap
@@ -4,14 +4,14 @@
             true,
             true,
             [
-                "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                "versions.yml:md5,b629089d44775078dce5e664a455422b"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-24T12:11:40.928513749"
+        "timestamp": "2024-12-03T07:57:01.869983435"
     },
     "ampcombi2_cluster - metagenome - stub": {
         "content": [
@@ -26,7 +26,7 @@
                     "Ampcombi_cluster.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "3": [
-                    "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                    "versions.yml:md5,b629089d44775078dce5e664a455422b"
                 ],
                 "cluster_tsv": [
                     "Ampcombi_summary_cluster.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -38,14 +38,14 @@
                     "Ampcombi_summary_cluster_representative_seq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                    "versions.yml:md5,b629089d44775078dce5e664a455422b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-24T12:12:08.780718892"
+        "timestamp": "2024-12-03T07:57:23.939137628"
     }
 }
diff --git a/modules/nf-core/ampcombi2/complete/environment.yml b/modules/nf-core/ampcombi2/complete/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"
diff --git a/modules/nf-core/ampcombi2/complete/main.nf b/modules/nf-core/ampcombi2/complete/main.nf
@@ -4,8 +4,8 @@ process AMPCOMBI2_COMPLETE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     path(summaries)

diff --git a/modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap b/modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap
@@ -6,39 +6,39 @@
                     "Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                    "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
                 ],
                 "log": [
-                    
+
                 ],
                 "tsv": [
                     "Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                    "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-29T11:55:16.030399422"
+        "timestamp": "2024-12-03T07:57:53.385349848"
     },
     "ampcombi2_complete - contigs": {
         "content": [
             true,
             [
-                "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-29T11:54:54.334224301"
+        "timestamp": "2024-12-03T07:57:40.263912946"
     }
-}
+}
diff --git a/modules/nf-core/ampcombi2/parsetables/environment.yml b/modules/nf-core/ampcombi2/parsetables/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"
diff --git a/modules/nf-core/ampcombi2/parsetables/main.nf b/modules/nf-core/ampcombi2/parsetables/main.nf
@@ -1,48 +1,54 @@
 process AMPCOMBI2_PARSETABLES {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(amp_input)
-    path(faa_input)
-    path(gbk_input)
-    path(opt_amp_db)
+    path faa_input
+    path gbk_input
+    val opt_amp_db
+    path opt_amp_db_dir
+    path opt_interproscan
 
     output:
-    tuple val(meta), path("${meta.id}/")                              , emit: sample_dir
-    tuple val(meta), path("${meta.id}/contig_gbks/")                  , emit: contig_gbks
-    tuple val(meta), path("${meta.id}/${meta.id}_diamond_matches.txt"), emit: txt
-    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.tsv")       , emit: tsv
-    tuple val(meta), path("${meta.id}/${meta.id}_amp.faa")            , emit: faa
-    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.log")       , emit: sample_log, optional:true
-    tuple val(meta), path("Ampcombi_parse_tables.log")                , emit: full_log, optional:true
-    tuple val(meta), path("amp_ref_database/")                        , emit: results_db, optional:true
-    tuple val(meta), path("amp_ref_database/*.dmnd")                  , emit: results_db_dmnd, optional:true
-    tuple val(meta), path("amp_ref_database/*.clean.fasta")           , emit: results_db_fasta, optional:true
-    tuple val(meta), path("amp_ref_database/*.tsv")                   , emit: results_db_tsv, optional:true
-    path "versions.yml"                                               , emit: versions
+    tuple val(meta), path("${meta.id}/")                                , emit: sample_dir
+    tuple val(meta), path("${meta.id}/contig_gbks/")                    , emit: contig_gbks
+    tuple val(meta), path("${meta.id}/${meta.id}_mmseqs_matches.tsv")   , emit: db_tsv
+    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.tsv")         , emit: tsv
+    tuple val(meta), path("${meta.id}/${meta.id}_amp.faa")              , emit: faa
+    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.log")         , emit: sample_log   , optional:true
+    tuple val(meta), path("Ampcombi_parse_tables.log")                  , emit: full_log     , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/")                , emit: db           , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/*.txt")           , emit: db_txt       , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/*.fasta")         , emit: db_fasta     , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/")        , emit: db_mmseqs    , optional:true
+    path "versions.yml"                                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def db = opt_amp_db? "--amp_database $opt_amp_db": ""
+    def db_dir = opt_amp_db_dir ? "--amp_database_dir ${opt_amp_db_dir}" : ""
+    def interpro = opt_interproscan ? "--interproscan_output ${opt_interproscan}" : ""
+
     """
     ampcombi parse_tables \\
-    --path_list '${amp_input.collect{"$it"}.join("' '")}' \\
-    --faa ${faa_input} \\
-    --gbk ${gbk_input} \\
-    --sample_list ${prefix} \\
-    ${db} \\
-    $args \\
-    --threads ${task.cpus}
+        --path_list '${amp_input.collect { "${it}" }.join("' '")}' \\
+        --faa ${faa_input} \\
+        --gbk ${gbk_input} \\
+        --sample_list ${prefix} \\
+        --amp_database ${opt_amp_db} \\
+        ${db_dir} \\
+        ${interpro} \\
+        ${args} \\
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -53,20 +59,30 @@ process AMPCOMBI2_PARSETABLES {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def db = opt_amp_db? "--amp_database $opt_amp_db": ""
+    def db_dir = opt_amp_db_dir ? "--amp_database_dir ${opt_amp_db_dir}" : ""
+    def interpro = opt_interproscan ? "--interproscan_output ${opt_interproscan}" : ""
+
     """
     mkdir -p ${prefix}
     mkdir -p ${prefix}/contig_gbks
-    touch ${prefix}/${meta.id}_diamond_matches.txt
+    touch ${prefix}/${meta.id}_mmseqs_matches.tsv
     touch ${prefix}/${meta.id}_ampcombi.tsv
     touch ${prefix}/${meta.id}_amp.faa
     touch ${prefix}/${meta.id}_ampcombi.log
     touch Ampcombi_parse_tables.log
 
-    mkdir -p amp_ref_database
-    touch amp_ref_database/*.dmnd
-    touch amp_ref_database/*.clean.fasta
-    touch amp_ref_database/*.tsv
+    mkdir -p amp_${opt_amp_db}_database
+    mkdir -p amp_${opt_amp_db}_database/mmseqs2
+    touch amp_${opt_amp_db}_database/*.fasta
+    touch amp_${opt_amp_db}_database/*.txt
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.dbtype
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.dbtype
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.index
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.index
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.lookup
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.source
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":