First pass at POC for topics update for bwamem2 and dependencies

.github/workflows/lint.yml

@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "25.04.6"
 
 jobs:
   pre-commit:

.github/workflows/nf-test-gpu.yml

@@ -30,7 +30,7 @@ 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: "25.04.0"
+  NXF_VER: "25.04.6"
 
 jobs:
   nf-test-changes:

.github/workflows/nf-test.yml

@@ -28,7 +28,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "25.04.0"
+  NXF_VER: "25.04.6"
 
 jobs:
   nf-test-changes:

.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_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   pytest-changes:

.github/workflows/update-gpu-snapshot.yml

@@ -10,7 +10,7 @@ env:
   NFT_VER: "0.9.2"
   NXF_ANSI_LOG: false
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   update-gpu-snapshot:

.github/workflows/update-sentieon-snapshot.yml

@@ -10,7 +10,7 @@ env:
   NFT_VER: "0.9.2"
   NXF_ANSI_LOG: false
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.2"
+  NXF_VER: "25.04.6"
 
 jobs:
   update-sentieon-snapshot:

.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_VER: "24.10.1"
+  NXF_VER: "25.04.6"
 
 jobs:
   generate-matrix:

modules/nf-core/bwamem2/index/main.nf

@@ -1,20 +1,20 @@
 process BWAMEM2_INDEX {
-    tag "$fasta"
+    tag "${fasta}"
     // NOTE Requires 28N GB memory where N is the size of the reference sequence, floor of 280M
     // source: https://github.com/bwa-mem2/bwa-mem2/issues/9
     memory { (280.MB * Math.ceil(fasta.size() / 10000000)) * task.attempt }
 
     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/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' :
-        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data'
+        : 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113'}"
 
     input:
     tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path("bwamem2"), emit: index
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('bwa-mem2'), eval("bwa-mem2 version 2>&1 | tail -1"), topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,14 +26,9 @@ process BWAMEM2_INDEX {
     mkdir bwamem2
     bwa-mem2 \\
         index \\
-        $args \\
+        ${args} \\
         -p bwamem2/${prefix} \\
-        $fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-    END_VERSIONS
+        ${fasta}
     """
 
     stub:
@@ -46,10 +41,5 @@ process BWAMEM2_INDEX {
     touch bwamem2/${prefix}.pac
     touch bwamem2/${prefix}.amb
     touch bwamem2/${prefix}.bwt.2bit.64
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-    END_VERSIONS
     """
 }

modules/nf-core/bwamem2/index/meta.yml

@@ -39,13 +39,6 @@ output:
           pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
           ontologies:
             - edam: "http://edamontology.org/data_3210" # Genome index
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@maxulysse"
 maintainers:

modules/nf-core/bwamem2/index/tests/main.nf.test

@@ -22,12 +22,11 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(
                     process.out.index,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    ['versions', process.out[1]]
                 ).match() }
             )
         }
@@ -49,12 +48,11 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(
                     process.out.index,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    ['versions', process.out[1]]
                 ).match() }
             )
         }

modules/nf-core/bwamem2/index/tests/main.nf.test.snap

@@ -16,19 +16,21 @@
                 ]
             ],
             [
-                "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
-            ],
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                }
-            }
+                "versions",
+                [
+                    [
+                        "BWAMEM2_INDEX",
+                        "bwa-mem2",
+                        "2.2.1"
+                    ]
+                ]
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-04T08:55:53.219699135"
+        "timestamp": "2025-09-25T14:38:35.557107186"
     },
     "fasta": {
         "content": [
@@ -47,18 +49,20 @@
                 ]
             ],
             [
-                "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
-            ],
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                }
-            }
+                "versions",
+                [
+                    [
+                        "BWAMEM2_INDEX",
+                        "bwa-mem2",
+                        "2.2.1"
+                    ]
+                ]
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-04T08:55:45.007921901"
+        "timestamp": "2025-09-25T14:38:22.536156282"
     }
 }

modules/nf-core/bwamem2/mem/main.nf

@@ -1,25 +1,26 @@
 process BWAMEM2_MEM {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     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/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' :
-        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data'
+        : 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113'}"
 
     input:
     tuple val(meta), path(reads)
     tuple val(meta2), path(index)
     tuple val(meta3), path(fasta)
-    val   sort_bam
+    val sort_bam
 
     output:
-    tuple val(meta), path("*.sam")  , emit: sam , optional:true
-    tuple val(meta), path("*.bam")  , emit: bam , optional:true
-    tuple val(meta), path("*.cram") , emit: cram, optional:true
-    tuple val(meta), path("*.crai") , emit: crai, optional:true
-    tuple val(meta), path("*.csi")  , emit: csi , optional:true
-    path  "versions.yml"            , emit: versions
+    tuple val(meta), path("*.sam"),  emit: sam,  optional: true
+    tuple val(meta), path("*.bam"),  emit: bam,  optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,  optional: true
+    tuple val("${task.process}"), val('bwa-mem2'), eval("bwa-mem2 version 2>&1 | tail -1"),                            topic: versions
+    tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -1 | sed 's/^.*samtools //'"), topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,53 +32,45 @@ process BWAMEM2_MEM {
     def samtools_command = sort_bam ? 'sort' : 'view'
 
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension_matcher = (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    def reference = fasta && extension == "cram" ? "--reference ${fasta}" : ""
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
     bwa-mem2 \\
         mem \\
-        $args \\
-        -t $task.cpus \\
+        ${args} \\
+        -t ${task.cpus} \\
         \$INDEX \\
-        $reads \\
-        | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} -
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+        ${reads} \\
+        | samtools ${samtools_command} ${args2} -@ ${task.cpus} ${reference} -o ${prefix}.${extension} -
     """
 
     stub:
-
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension_matcher = (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     def create_index = ""
     if (extension == "cram") {
         create_index = "touch ${prefix}.crai"
-    } else if (extension == "bam") {
+    }
+    else if (extension == "bam") {
         create_index = "touch ${prefix}.csi"
     }
 
     """
     touch ${prefix}.${extension}
     ${create_index}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/bwamem2/mem/meta.yml

@@ -118,13 +118,6 @@ output:
           description: Index file for BAM file
           pattern: "*.{csi}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@maxulysse"
   - "@matthdsm"