Merge branch 'master' into functional_analysis

.github/actions/nf-test-action/action.yml

@@ -17,7 +17,7 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+    - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
       with:
         distribution: "temurin"
         java-version: "17"

.github/workflows/gpu-tests.yml

@@ -103,7 +103,7 @@ jobs:
           total_shards: ${{ env.TOTAL_SHARDS }}
           paths: "${{ join(fromJson(needs.nf-test-changes.outputs.paths), ' ') }}"
 
-  confirm-pass:
+  confirm-pass-gpu:
     runs-on: ubuntu-latest
     needs: [nf-test-gpu]
     if: always()

.github/workflows/lint.yml

@@ -120,7 +120,7 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
         with:
           distribution: "temurin"
           java-version: "17"

.github/workflows/pytest-workflow.yml

@@ -258,7 +258,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4
         with:
           distribution: "temurin"
           java-version: "17"
@@ -308,7 +308,7 @@ jobs:
 
       - name: Upload logs on failure
         if: failure()
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b # v4
         with:
           name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
           path: |

.github/workflows/wave.yml

@@ -31,7 +31,7 @@ jobs:
 
       - name: Find conda differences
         id: conda-diff
-        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
+        uses: tj-actions/changed-files@d6e91a2266cdb9d62096cebf1e8546899c6aa18f # v45
         with:
           json: true
           escape_json: false
@@ -40,7 +40,7 @@ jobs:
 
       - name: Find Dockerfile differences
         id: docker-diff
-        uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45
+        uses: tj-actions/changed-files@d6e91a2266cdb9d62096cebf1e8546899c6aa18f # v45
         with:
           json: true
           escape_json: false

modules/nf-core/affy/justrma/templates/affy_justrma.R

@@ -54,7 +54,7 @@ read_delim_flexible <- function(file, header = TRUE, row.names = NULL){
 #' Install the right CDF for a given cel file
 #'
 #' @param celfile A valid path to a CEL file
-#' @param annotation Boolean indication wheter to install the annotation
+#' @param annotation Boolean indication whether to install the annotation
 #'        package
 #'
 #' @return output The CDF environment or a list detailing the failed locations.

modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml

@@ -37,7 +37,7 @@ input:
   - - config:
         type: file
         description: |
-          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
         pattern: "*.yaml"
 output:
   - gff:

modules/nf-core/agat/spmergeannotations/meta.yml

@@ -31,7 +31,7 @@ input:
         type: file
         description: |
           Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,
-          otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml
+          otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml
           locally type: "agat config --expose". The --config option gives you the possibility to use your
           own AGAT config file (located elsewhere or named differently).
         pattern: "*.yaml"

modules/nf-core/agrvate/meta.yml

@@ -33,12 +33,12 @@ output:
             e.g. [ id:'test', single_end:false ]
       - ${fasta.baseName}-results/${fasta.baseName}-summary.tab:
           type: file
-          description: A summary of the agrvate assessement
+          description: A summary of the agrvate assessment
           pattern: "*-summary.tab"
   - results_dir:
       - ${fasta.baseName}-results:
           type: directory
-          description: Results of the agrvate assessement
+          description: Results of the agrvate assessment
           pattern: "*-results"
   - versions:
       - versions.yml:

modules/nf-core/ampcombi/meta.yml

@@ -155,7 +155,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - amp_ref_database/*.clean.fasta:
           type: file
-          description: AMP reference database fasta file, cleaned of diamond-uncompatible
+          description: AMP reference database fasta file, cleaned of diamond-incompatible
             characters.
           pattern: "/amp_ref_database/*.clean.fasta"
   - results_db_tsv:

modules/nf-core/ampcombi2/parsetables/meta.yml

@@ -176,7 +176,6 @@ output:
       - amp_${opt_amp_db}_database/*.fasta:
           type: file
           description: AMP reference database fasta file in clean format.
-            characters.
           pattern: "/amp_*_database/*.fasta"
   - db_mmseqs:
       - meta:

modules/nf-core/annotsv/annotsv/main.nf

@@ -4,8 +4,8 @@ process ANNOTSV_ANNOTSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     input:
     tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants)

modules/nf-core/annotsv/installannotations/main.nf

@@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     output:
     path "AnnotSV_annotations", emit: annotations

modules/nf-core/arriba/download/meta.yml

@@ -36,13 +36,13 @@ output:
       - protein_domains*${genome}*.gff3:
           type: file
           description: Protein domain annotations
-          patter: "*.gff3"
+          pattern: "*.gff3"
   - known_fusions:
       - known_fusions*${genome}*.tsv.gz:
           type: file
           description: Arriba is more sensitive to those fusions to improve the detection
             rate of expected or highly relevant events, such as recurrent fusions
-          patter: "*.tsv.gz"
+          pattern: "*.tsv.gz"
   - versions:
       - versions.yml:
           type: file

modules/nf-core/arriba/download/tests/main.nf.test.snap

@@ -1,5 +1,5 @@
 {
-    "download": {
+    "test-arriba-download": {
         "content": [
             {
                 "0": [
@@ -35,9 +35,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-08T11:12:17.010496"
+        "timestamp": "2024-12-16T01:46:32.110653034"
     }
 }

modules/nf-core/bakta/bakta/meta.yml

@@ -103,7 +103,7 @@ output:
       - ${prefix}.hypotheticals.tsv:
           type: file
           description: additional information on hypothetical protein CDS as simple human
-            readble tab separated values
+            readable tab separated values
           pattern: "*.hypotheticals.tsv"
   - hypotheticals_faa:
       - meta:
@@ -123,7 +123,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - ${prefix}.tsv:
           type: file
-          description: annotations as simple human readble tab separated values
+          description: annotations as simple human readable tab separated values
           pattern: "*.tsv"
   - txt:
       - meta:

modules/nf-core/bbmap/align/main.nf

@@ -26,7 +26,7 @@ process BBMAP_ALIGN {
     input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
 
     // Set the db variable to reflect the three possible types of reference input: 1) directory
-    // named 'ref', 2) directory named something else (containg a 'ref' subdir) or 3) a sequence
+    // named 'ref', 2) directory named something else (containing a 'ref' subdir) or 3) a sequence
     // file in fasta format
     if ( ref.isDirectory() ) {
         if ( ref ==~ /(.\/)?ref\/?/ ) {
@@ -48,6 +48,19 @@ process BBMAP_ALIGN {
         -Xmx${task.memory.toGiga()}g \\
         &> ${prefix}.bbmap.log
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.bbmap.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")

modules/nf-core/bbmap/align/meta.yml

@@ -31,7 +31,7 @@ input:
         description: |
           Either "ref" a directory containing an index, the name of another directory
           with a "ref" subdirectory containing an index or the name of a fasta formatted
-          nucleotide file containg the reference to map to.
+          nucleotide file containing the reference to map to.
 output:
   - bam:
       - meta: