Merge branch 'nf-core:master' into parabricks-sbwf

nf-core · Jan 31, 2025 · 656fca3 · 656fca3
2 parents 2a7d739 + 94ca1fd
commit 656fca3
Show file tree

Hide file tree

Showing 47 changed files with 1,590 additions and 569 deletions.
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
@@ -17,7 +17,6 @@ outputs:
   total_shards:
     description: "Total number of shards"
     value: ${{ steps.shards.outputs.total_shards }}
-
 runs:
   using: "composite"
   steps:
@@ -26,22 +25,24 @@ runs:
       with:
         version: ${{ env.NFT_VER }}
         install-pdiff: true
-
     - name: Get number of shards
       id: shards
       shell: bash
       run: |
-
         # Prepare tag parameter if tags are provided
         TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
-        # Run nf-test with dynamic tag parameter
+
+        # Run nf-test with dynamic parameter
         nftest_output=$(nf-test test \
           --dry-run \
           --profile docker \
           ${TAGS} \
           --filter process,workflow \
-          ${{ inputs.paths }})
-
+          ${{ inputs.paths }}) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
         echo "nf-test dry-run output: $nftest_output"
 
         # Default values for shard and total_shards

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
+    - uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
       with:
         distribution: "temurin"
         java-version: "17"
@@ -28,7 +28,7 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
       with:
         python-version: "3.11"
 

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         with:
           extra_args: ""
@@ -113,7 +113,7 @@ jobs:
           sudo rm -rf ./.* || true
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
           python-version: "3.11"
 
@@ -128,7 +128,7 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
+      - uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
         with:
           distribution: "temurin"
           java-version: "17"

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -193,3 +193,11 @@ jobs:
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "DEBUG: needs.nf-test.outputs.filtered_paths = ${{ needs.nf-test.outputs.filtered_paths }}"
           echo "::endgroup::"
+
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -243,7 +243,7 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
           python-version: "3.11"
 
@@ -258,7 +258,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
+      - uses: actions/setup-java@3a4f6e1af504cf6a31855fa899c6aa5355ba6c12 # v4
         with:
           distribution: "temurin"
           java-version: "17"

diff --git a/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r b/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r
@@ -327,12 +327,11 @@ ads <- do.call(anota2seqDataSetFromMatrix, anota2seqDataSetFromMatrix_args)
 # Run anota2seqRun
 
 contrast_matrix <- matrix(
-    nrow=2,
-    ncol=1,
-    dimnames=list(c(opt\$reference_level, opt\$target_level),c()),
-    c(-1,1)
+    c(-1, 1),
+    nrow = 2,
+    dimnames = list(sort(c(opt\$reference_level, opt\$target_level)), NULL)
 )
-
+                                                                                 
 ads <- anota2seqRun(
     ads,
     contrasts = contrast_matrix,

diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf
@@ -1,44 +1,45 @@
 process ANTISMASH_ANTISMASHLITE {
-    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/antismash-lite:7.1.0--pyhdfd78af_0' :
-        'biocontainers/antismash-lite:7.1.0--pyhdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/antismash-lite:7.1.0--pyhdfd78af_0'
+        : 'biocontainers/antismash-lite:7.1.0--pyhdfd78af_0'}"
 
     containerOptions {
-        workflow.containerEngine == 'singularity' ?
-        "-B $antismash_dir:/usr/local/lib/python3.10/site-packages/antismash" :
-        workflow.containerEngine == 'docker' ?
-        "-v \$PWD/$antismash_dir:/usr/local/lib/python3.10/site-packages/antismash" :
-        ''
-        }
+        ['singularity', 'apptainer'].contains(workflow.containerEngine)
+            ? "-B ${antismash_dir}:/usr/local/lib/python3.10/site-packages/antismash"
+            : workflow.containerEngine == 'docker'
+                ? "-v \$PWD/${antismash_dir}:/usr/local/lib/python3.10/site-packages/antismash"
+                : ''
+    }
 
     input:
     tuple val(meta), path(sequence_input)
-    path(databases)
-    path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
-    path(gff)
+    path databases
+    path antismash_dir
+    // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
+    path gff
 
     output:
-    tuple val(meta), path("${prefix}/clusterblast/*_c*.txt")                 , optional: true, emit: clusterblast_file
-    tuple val(meta), path("${prefix}/{css,images,js}")                       , emit: html_accessory_files
-    tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html")   , optional: true, emit: knownclusterblast_html
-    tuple val(meta), path("${prefix}/knownclusterblast/")                    , optional: true, emit: knownclusterblast_dir
-    tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt")            , optional: true, emit: knownclusterblast_txt
-    tuple val(meta), path("${prefix}/svg/clusterblast*.svg")                 , optional: true, emit: svg_files_clusterblast
-    tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg")            , optional: true, emit: svg_files_knownclusterblast
-    tuple val(meta), path("${prefix}/*.gbk")                                 , emit: gbk_input
-    tuple val(meta), path("${prefix}/*.json")                                , emit: json_results
-    tuple val(meta), path("${prefix}/*.log")                                 , emit: log
-    tuple val(meta), path("${prefix}/*.zip")                                 , emit: zip
-    tuple val(meta), path("${prefix}/*region*.gbk")                          , optional: true, emit: gbk_results
-    tuple val(meta), path("${prefix}/clusterblastoutput.txt")                , optional: true, emit: clusterblastoutput
-    tuple val(meta), path("${prefix}/index.html")                            , emit: html
-    tuple val(meta), path("${prefix}/knownclusterblastoutput.txt")           , optional: true, emit: knownclusterblastoutput
-    tuple val(meta), path("${prefix}/regions.js")                            , emit: json_sideloading
-    path "versions.yml"                                                      , emit: versions
+    tuple val(meta), path("${prefix}/clusterblast/*_c*.txt"), optional: true, emit: clusterblast_file
+    tuple val(meta), path("${prefix}/{css,images,js}"), emit: html_accessory_files
+    tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html"), optional: true, emit: knownclusterblast_html
+    tuple val(meta), path("${prefix}/knownclusterblast/"), optional: true, emit: knownclusterblast_dir
+    tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt"), optional: true, emit: knownclusterblast_txt
+    tuple val(meta), path("${prefix}/svg/clusterblast*.svg"), optional: true, emit: svg_files_clusterblast
+    tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg"), optional: true, emit: svg_files_knownclusterblast
+    tuple val(meta), path("${prefix}/*.gbk"), emit: gbk_input
+    tuple val(meta), path("${prefix}/*.json"), emit: json_results
+    tuple val(meta), path("${prefix}/*.log"), emit: log
+    tuple val(meta), path("${prefix}/*.zip"), emit: zip
+    tuple val(meta), path("${prefix}/*region*.gbk"), optional: true, emit: gbk_results
+    tuple val(meta), path("${prefix}/clusterblastoutput.txt"), optional: true, emit: clusterblastoutput
+    tuple val(meta), path("${prefix}/index.html"), emit: html
+    tuple val(meta), path("${prefix}/knownclusterblastoutput.txt"), optional: true, emit: knownclusterblastoutput
+    tuple val(meta), path("${prefix}/regions.js"), emit: json_sideloading
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -53,25 +54,24 @@ process ANTISMASH_ANTISMASHLITE {
     ## this should be run as a separate module for versioning purposes
 
     antismash \\
-        $args \\
-        $gff_flag \\
-        -c $task.cpus \\
-        --output-dir $prefix \\
-        --output-basename $prefix \\
+        ${args} \\
+        ${gff_flag} \\
+        -c ${task.cpus} \\
+        --output-dir ${prefix} \\
+        --output-basename ${prefix} \\
         --genefinding-tool none \\
-        --logfile $prefix/${prefix}.log \\
-        --databases $databases \\
-        $sequence_input
+        --logfile ${prefix}/${prefix}.log \\
+        --databases ${databases} \\
+        ${sequence_input}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //')
+        antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g')
     END_VERSIONS
     """
 
     stub:
     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
-    def VERSION = '7.1.0' // WARN: Version information not provided by tool during stub run. Please update this string when bumping container versions.
     """
     mkdir -p ${prefix}/css
     mkdir ${prefix}/images
@@ -91,7 +91,7 @@ process ANTISMASH_ANTISMASHLITE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        antismash-lite: $VERSION
+        antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test b/modules/nf-core/antismash/antismashlite/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process ANTISMASH_ANTISMASHLITE"
     script "../main.nf"
     process "ANTISMASH_ANTISMASHLITE"
+    config './nextflow.config'
 
     tag "modules"
     tag "modules_nfcore"
@@ -96,7 +97,11 @@ nextflow_process {
                 { assert path(process.out.html.get(0).get(1)).text.contains("https://antismash.secondarymetabolites.org/") },
                 { assert path(process.out.json_sideloading.get(0).get(1)).text.contains("\"seq_id\": \"NZ_CP069563.1\"") },
                 { assert path(process.out.log.get(0).get(1)).text.contains("antiSMASH status: SUCCESS") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(
+                    path(process.out.versions[0]).yaml,
+                    file(process.out.versions[0]).name,
+                    ).match("versions")
+                }
             )
         }
     }
@@ -119,7 +124,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    file(process.out.versions[0]).name,
+                    ).match("versions_stub")
+                }
             )
         }
     }