fix clairs indel calling

.github/workflows/linting.yml

@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.prettierignore

@@ -10,4 +10,7 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/

conf/modules.config

@@ -168,18 +168,20 @@ process {
             ].join(' ').trim()
         }
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/methylation/${meta.type}/fibertoolsrs/predictm6a" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            enabled: false
         ]
     }
 
     withName: '.*:FIBERTOOLSRS_FIRE' {
         ext.args   = { (meta.platform == "ont") ? "--ont" : "" }
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/methylation/${meta.type}/fibertoolsrs/fire" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            enabled: false
+        ]
+    }
+
+    withName: '.*:FIBERTOOLSRS_NUCLEOSOMES' {
+        publishDir = [
+            enabled: false
         ]
     }
 
@@ -224,7 +226,18 @@ process {
     //
     // Small variant calling processes
     //
-
+    withName: '.*:BCFTOOLS_CONCAT' {
+        ext.args = '--output-type z -a'
+        publishDir = [
+            enabled: false
+        ]
+    }
+    withName: '.*:BCFTOOLS_SORT' {
+        ext.arge = '--output-type z'
+        publishDir = [
+            enabled: false
+        ]
+    }
     withName: '.*:CLAIRSTO' {
         publishDir = [
             path: { "${params.outdir}/${meta.id}/variants/clairsto" },
@@ -234,6 +247,7 @@ process {
     }
 
     withName: '.*:CLAIRS' {
+        ext.args = '--enable_indel_calling --haplotagged_tumor_bam_provided_so_skip_intermediate_phasing_and_haplotagging'
         publishDir = [
             path: { "${params.outdir}/${meta.id}/variants/clairs" },
             mode: params.publish_dir_mode,

modules.json

@@ -11,6 +11,22 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/ascat/ascat.diff"
                     },
+                    "bcftools/concat": {
+                        "branch": "master",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "installed_by": ["modules", "vcf_gather_bcftools"]
+                    },
+                    "bcftools/merge": {
+                        "branch": "master",
+                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
+                        "installed_by": ["modules"]
+                    },
+                    "bcftools/sort": {
+                        "branch": "master",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "installed_by": ["vcf_gather_bcftools"],
+                        "patch": "modules/nf-core/bcftools/sort/bcftools-sort.diff"
+                    },
                     "ensemblvep/download": {
                         "branch": "master",
                         "git_sha": "2fcc53751152a999bfc9c24f75f494b9e5bb338f",

modules/local/clairs/main.nf

@@ -12,9 +12,9 @@ process CLAIRS {
     tuple val(meta3), path(index)
 
     output:
-    tuple val(meta), path("*.vcf.gz"),      emit: vcf
-    tuple val(meta), path("*.vcf.gz.tbi"),  emit: tbi
-    path "versions.yml",                    emit: versions
+    tuple val(meta), path("*.vcf.gz"),               emit: vcfs
+    tuple val(meta), path("*.vcf.gz.tbi"),           emit: tbi
+    path "versions.yml",                             emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,9 +31,14 @@ process CLAIRS {
         --threads $task.cpus \\
         --platform $model \\
         --output_dir . \\
-        --output_prefix $prefix \\
+        --output_prefix snvs \\
         $args
 
+    if [[ -f "snv.vcf.gz" ]]; then
+        rm snv.vcf.gz
+        rm snv.vcf.gz.tbi
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         clairs: \$(/opt/bin/run_clairs  --version |& sed '1!d ; s/run_clairs //')
@@ -45,8 +50,8 @@ process CLAIRS {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    echo "" | gzip > ${prefix}.vcf.gz
-    touch ${prefix}.vcf.gz.tbi
+    echo "" | gzip > snv.vcf.gz
+    touch snv.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/metaextract/main.nf

@@ -11,8 +11,8 @@ process METAEXTRACT {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), env(basecall_model),env(kinetics)  , emit: meta_ext
-    path "versions.yml"                        , emit: versions
+    tuple val(meta), env(basecall_model), env(kinetics)  , emit: meta_ext
+    path "versions.yml"                                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when