Varscan topic

modules/nf-core/varscan/fpfilter/main.nf

@@ -13,7 +13,7 @@ process VARSCAN_FPFILTER {
     output:
     tuple val(meta), path("*.pass.vcf.gz"), emit: pass_vcf
     tuple val(meta), path("*.fail.vcf.gz"), emit: fail_vcf
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('varscan'), eval("varscan 2>&1 | sed -n '2s/.*v//p'"), emit: versions_varscan, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,11 +34,6 @@ process VARSCAN_FPFILTER {
 
     bgzip ${prefix}.pass.vcf
     bgzip ${prefix}.fail.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        varscan: \$(varscan 2>&1 | grep VarScan | head -n 1 | sed 's/VarScan //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
-    END_VERSIONS
     """
 
     stub:
@@ -49,10 +44,5 @@ process VARSCAN_FPFILTER {
 
     echo "" | gzip > ${prefix}.pass.vcf.gz
     echo "" | gzip > ${prefix}.fail.vcf.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        varscan: \$(varscan 2>&1 | grep VarScan | head -n 1 | sed 's/VarScan //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
-    END_VERSIONS
     """
 }

modules/nf-core/varscan/fpfilter/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "varscan_fpfilter"
 description: VarScan2 is a tool for variant detection in massively parallel
   sequencing data. It can detect SNPs, indels, and copy number variations in
@@ -19,9 +18,9 @@ tools:
       documentation: "https://dkoboldt.github.io/varscan/"
       tool_dev_url: "https://github.com/dkoboldt/varscan"
       doi: "10.1101/gr.129684.111"
-      licence: ["The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"]
+      licence:
+        - "The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"
       identifier: biotools:varscan
-
 input:
   - - meta:
         type: map
@@ -34,7 +33,7 @@ input:
         pattern: "*.vcf.gz"
         ontologies:
           - edam: "http://edamontology.org/format_3016" # VCF
-          - edam: "http://edamontology.org/format_3989" # GZIP format
+          - edam: "http://edamontology.org/format_3989" # GZIP
     - rc:
         type: file
         description: Read counts file from bam-readcount
@@ -53,7 +52,7 @@ output:
           pattern: "*.pass.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
   fail_vcf:
     - - meta:
           type: map
@@ -66,14 +65,30 @@ output:
           pattern: "*.fail.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
+  versions_varscan:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - varscan:
+          type: string
+          description: The name of the tool
+      - varscan 2>&1 | sed -n '2s/.*v//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: versions.yml
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - varscan:
+          type: string
+          description: The name of the tool
+      - varscan 2>&1 | sed -n '2s/.*v//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@vmelichar"
 maintainers:

modules/nf-core/varscan/fpfilter/tests/main.nf.test

@@ -86,7 +86,7 @@ nextflow_process {
                     assert snapshot(
                         path(process.out.pass_vcf.get(0).get(1)).vcf.variantsMD5,
                         path(process.out.fail_vcf.get(0).get(1)).vcf.variantsMD5,
-                        process.out.versions,
+                        sanitizeOutput(process.out, unstableKeys: ["vcf"]),
                     ).match()
                 }
             )

modules/nf-core/varscan/fpfilter/tests/main.nf.test.snap

@@ -21,7 +21,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,93abb838631426ac5528b39b1e867481"
+                    [
+                        "VARSCAN_FPFILTER",
+                        "varscan",
+                        "2.4.6"
+                    ]
                 ],
                 "fail_vcf": [
                     [
@@ -41,29 +45,57 @@
                         "test.pass.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,93abb838631426ac5528b39b1e867481"
+                "versions_varscan": [
+                    [
+                        "VARSCAN_FPFILTER",
+                        "varscan",
+                        "2.4.6"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-06-18T12:20:29.020655376",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-07-28T10:17:06.573224273"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "human - mpileup": {
         "content": [
             "8e1b97375c4d8501f3873496b80a4dc9",
             "55341b65671b6af9cde4309b2f7033ce",
-            [
-                "versions.yml:md5,93abb838631426ac5528b39b1e867481"
-            ]
+            {
+                "fail_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fail.vcf.gz:md5,dcfae92129fbc1134795e0fc32832d00"
+                    ]
+                ],
+                "pass_vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pass.vcf.gz:md5,ab67893779f5339be49a1dced06a7049"
+                    ]
+                ],
+                "versions_varscan": [
+                    [
+                        "VARSCAN_FPFILTER",
+                        "varscan",
+                        "2.4.6"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-06-18T12:20:19.24310901",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-07-28T15:52:46.081739882"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }

modules/nf-core/varscan/processsomatic/main.nf

@@ -17,7 +17,7 @@ process VARSCAN_PROCESSSOMATIC {
     tuple val(meta), path("*.Somatic.hc.vcf.gz") , emit: somatic_hc_vcf
     tuple val(meta), path("*.LOH.vcf.gz")        , emit: loh_vcf
     tuple val(meta), path("*.LOH.hc.vcf.gz")     , emit: loh_hc_vcf
-    path "versions.yml"                          , emit: versions
+    tuple val("${task.process}"), val('varscan'), eval("varscan 2>&1 | sed -n '2s/.*v//p'"), emit: versions_varscan, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,11 +32,6 @@ process VARSCAN_PROCESSSOMATIC {
         ${vcf.baseName}
 
     bgzip *.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        varscan: \$(varscan 2>&1 | grep VarScan | head -n 1 | sed 's/VarScan //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
-    END_VERSIONS
     """
 
     stub:
@@ -48,10 +43,5 @@ process VARSCAN_PROCESSSOMATIC {
     echo "" | gzip > ${output_name}.Somatic.hc.vcf.gz
     echo "" | gzip > ${output_name}.LOH.vcf.gz
     echo "" | gzip > ${output_name}.LOH.hc.vcf.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        varscan: \$(varscan 2>&1 | grep VarScan | head -n 1 | sed 's/VarScan //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
-    END_VERSIONS
     """
 }

modules/nf-core/varscan/processsomatic/meta.yml

@@ -1,11 +1,10 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "varscan_processsomatic"
 description: VarScan2 is a tool for variant detection in massively parallel
   sequencing data. It can detect SNPs, indels, and copy number variations in
   both somatic and germline samples. It is particularly useful for analyzing
   tumor/normal sample pairs. This subtool divides variants based on status
-  (germline, somatic, loss of heterozygosity) and confidence level (high-confidence
-  or not) and outputs them in separate VCF files.
+  (germline, somatic, loss of heterozygosity) and confidence level
+  (high-confidence or not) and outputs them in separate VCF files.
 keywords:
   - variant calling
   - germline
@@ -20,9 +19,9 @@ tools:
       documentation: "https://dkoboldt.github.io/varscan/"
       tool_dev_url: "https://github.com/dkoboldt/varscan"
       doi: "10.1101/gr.129684.111"
-      licence: ["The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"]
+      licence:
+        - "The Non-Profit Open Software License version 3.0 (NPOSL-3.0)"
       identifier: biotools:varscan
-
 input:
   - - meta:
         type: map
@@ -35,7 +34,7 @@ input:
         pattern: "*.{snvs,indels}.vcf.gz"
         ontologies:
           - edam: "http://edamontology.org/format_3016" # VCF
-          - edam: "http://edamontology.org/format_3989" # GZIP format
+          - edam: "http://edamontology.org/format_3989" # GZIP
 output:
   germline_vcf:
     - - meta:
@@ -49,7 +48,7 @@ output:
           pattern: "*.Germline.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
   germline_hc_vcf:
     - - meta:
           type: map
@@ -62,7 +61,7 @@ output:
           pattern: "*.Germline.hc.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
   somatic_vcf:
     - - meta:
           type: map
@@ -75,7 +74,7 @@ output:
           pattern: "*.Somatic.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
   somatic_hc_vcf:
     - - meta:
           type: map
@@ -88,7 +87,7 @@ output:
           pattern: "*.Somatic.hc.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
   loh_vcf:
     - - meta:
           type: map
@@ -101,7 +100,7 @@ output:
           pattern: "*.LOH.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
   loh_hc_vcf:
     - - meta:
           type: map
@@ -115,14 +114,30 @@ output:
           pattern: "*.LOH.hc.vcf.gz"
           ontologies:
             - edam: "http://edamontology.org/format_3016" # VCF
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: "http://edamontology.org/format_3989" # GZIP
+  versions_varscan:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - varscan:
+          type: string
+          description: The name of the tool
+      - varscan 2>&1 | sed -n '2s/.*v//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - varscan:
+          type: string
+          description: The name of the tool
+      - varscan 2>&1 | sed -n '2s/.*v//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@vmelichar"
 maintainers:

modules/nf-core/varscan/processsomatic/tests/main.nf.test

@@ -50,7 +50,7 @@ nextflow_process {
                         path(process.out.somatic_hc_vcf.get(0).get(1)).vcf.variantsMD5,
                         path(process.out.loh_vcf.get(0).get(1)).vcf.variantsMD5,
                         path(process.out.loh_hc_vcf.get(0).get(1)).vcf.variantsMD5,
-                        process.out.versions,
+                        process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )