Syntax updates and topic version for manta modules

modules/nf-core/manta/convertinversion/environment.yml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=2.7.15
-  - bioconda::manta=1.6.0
   - bioconda::htslib=1.16
+  - bioconda::manta=1.6.0
   - bioconda::samtools=1.16.1
+  - conda-forge::python=2.7.15

modules/nf-core/manta/convertinversion/main.nf

@@ -15,7 +15,8 @@ process MANTA_CONVERTINVERSION {
     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("${task.process}"), val("manta"), eval("configManta.py --version"), topic: versions, emit: versions_manta
+    tuple val("${task.process}"), val("samtools"), eval("samtools --version | head -1 | sed -e s'/samtools //'"), topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,24 +26,12 @@ process MANTA_CONVERTINVERSION {
     """
     convertInversion.py \$(which samtools) $fasta $vcf | bgzip --threads $task.cpus > ${prefix}.vcf.gz
     tabix ${prefix}.vcf.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        manta: \$( configManta.py --version )
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        manta: \$( configManta.py --version )
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
-    END_VERSIONS
     """
 }

modules/nf-core/manta/convertinversion/meta.yml

@@ -61,13 +61,48 @@ output:
           description: TBI file produces by Manta
           pattern: "*.vcf.gz.tbi"
           ontologies: []
+  versions_manta:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - manta:
+          type: string
+          description: The name of the tool
+      - configManta.py --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools --version | head -1 | sed -e s'/samtools //':
+          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
+      - manta:
+          type: string
+          description: The name of the tool
+      - configManta.py --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools --version | head -1 | sed -e s'/samtools //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@FriederikeHanssen"
 maintainers:

modules/nf-core/manta/convertinversion/tests/main.nf.test

@@ -57,7 +57,7 @@ nextflow_process {
                 { assert snapshot(
                     process.out.vcf.collect { it.collect { it instanceof Map ? it : path(it).linesGzip[-7..-3] } },
                     process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions_") }
                 ).match() }
             )
         }

modules/nf-core/manta/convertinversion/tests/main.nf.test.snap

@@ -19,7 +19,18 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d9a3c2c54bad36a8310d42eae3d57801"
+                    [
+                        "MANTA_CONVERTINVERSION",
+                        "manta",
+                        "1.6.0"
+                    ]
+                ],
+                "3": [
+                    [
+                        "MANTA_CONVERTINVERSION",
+                        "samtools",
+                        "1.16.1"
+                    ]
                 ],
                 "tbi": [
                     [
@@ -37,16 +48,27 @@
                         "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,d9a3c2c54bad36a8310d42eae3d57801"
+                "versions_manta": [
+                    [
+                        "MANTA_CONVERTINVERSION",
+                        "manta",
+                        "1.6.0"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "MANTA_CONVERTINVERSION",
+                        "samtools",
+                        "1.16.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-05-06T10:26:25.996091364"
+        "timestamp": "2025-12-11T16:58:38.212888433"
     },
     "homo_sapiens - vcf, fasta": {
         "content": [
@@ -72,14 +94,27 @@
                     "test.vcf.gz.tbi"
                 ]
             ],
-            [
-                "versions.yml:md5,d9a3c2c54bad36a8310d42eae3d57801"
-            ]
+            {
+                "versions_manta": [
+                    [
+                        "MANTA_CONVERTINVERSION",
+                        "manta",
+                        "1.6.0"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "MANTA_CONVERTINVERSION",
+                        "samtools",
+                        "1.16.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-17T09:41:08.582282"
+        "timestamp": "2025-12-11T17:02:58.806373235"
     }
 }

modules/nf-core/manta/germline/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=2.7.15
   - bioconda::manta=1.6.0
+  - conda-forge::python=2.7.15

modules/nf-core/manta/germline/main.nf

@@ -16,21 +16,21 @@ process MANTA_GERMLINE {
     path(config)
 
     output:
-    tuple val(meta), path("*candidate_small_indels.vcf.gz")    , emit: candidate_small_indels_vcf
-    tuple val(meta), path("*candidate_small_indels.vcf.gz.tbi"), emit: candidate_small_indels_vcf_tbi
-    tuple val(meta), path("*candidate_sv.vcf.gz")              , emit: candidate_sv_vcf
-    tuple val(meta), path("*candidate_sv.vcf.gz.tbi")          , emit: candidate_sv_vcf_tbi
-    tuple val(meta), path("*diploid_sv.vcf.gz")                , emit: diploid_sv_vcf
-    tuple val(meta), path("*diploid_sv.vcf.gz.tbi")            , emit: diploid_sv_vcf_tbi
-    path "versions.yml"                                        , emit: versions
+    tuple val(meta), path("*candidate_small_indels.vcf.gz")                     , emit: candidate_small_indels_vcf
+    tuple val(meta), path("*candidate_small_indels.vcf.gz.tbi")                 , emit: candidate_small_indels_vcf_tbi
+    tuple val(meta), path("*candidate_sv.vcf.gz")                               , emit: candidate_sv_vcf
+    tuple val(meta), path("*candidate_sv.vcf.gz.tbi")                           , emit: candidate_sv_vcf_tbi
+    tuple val(meta), path("*diploid_sv.vcf.gz")                                 , emit: diploid_sv_vcf
+    tuple val(meta), path("*diploid_sv.vcf.gz.tbi")                             , emit: diploid_sv_vcf_tbi
+    tuple val("${task.process}"), val("manta"), eval("configManta.py --version"), topic: versions, emit: versions_manta
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_files = input.collect{"--bam ${it}"}.join(' ')
+    def input_files = input.collect{ bam -> "--bam ${bam}"}.join(' ')
     def options_manta = target_bed ? "--callRegions $target_bed" : ""
     def config_option = config ? "--config ${config}" : ""
     """
@@ -56,11 +56,6 @@ process MANTA_GERMLINE {
         ${prefix}.diploid_sv.vcf.gz
     mv manta/results/variants/diploidSV.vcf.gz.tbi \\
         ${prefix}.diploid_sv.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        manta: \$( configManta.py --version )
-    END_VERSIONS
     """
 
     stub:
@@ -72,10 +67,5 @@ process MANTA_GERMLINE {
     touch ${prefix}.candidate_sv.vcf.gz.tbi
     echo "" | gzip > ${prefix}.diploid_sv.vcf.gz
     touch ${prefix}.diploid_sv.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        manta: \$( configManta.py --version )
-    END_VERSIONS
     """
 }

modules/nf-core/manta/germline/meta.yml

@@ -137,13 +137,29 @@ output:
           description: Index for gzipped VCF file containing variants
           pattern: "*.{vcf.gz.tbi}"
           ontologies: []
+  versions_manta:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - manta:
+          type: string
+          description: The name of the tool
+      - configManta.py --version:
+          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
+      - manta:
+          type: string
+          description: The name of the tool
+      - configManta.py --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@maxulysse"
   - "@ramprasadn"

modules/nf-core/manta/germline/tests/main.nf.test

@@ -42,7 +42,7 @@ nextflow_process {
                     path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
                     path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
                     path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions_") }
                 ).match() }
             )
         }
@@ -81,7 +81,7 @@ nextflow_process {
                     path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
                     path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
                     path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions_") }
                 ).match() }
             )
         }
@@ -124,7 +124,7 @@ nextflow_process {
                     path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
                     path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
                     path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"),
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions_") }
                 ).match() }
             )
         }