nf-core · SPPearce · Jul 8, 2026
diff --git a/modules/nf-core/strelka/germline/environment.yml b/modules/nf-core/strelka/germline/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=2.7.15
   - bioconda::strelka=2.9.10=h9ee0642_1
+  - conda-forge::python=2.7.15
diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf
@@ -18,7 +18,7 @@ process STRELKA_GERMLINE {
     tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi
     tuple val(meta), path("*genome.vcf.gz"),       emit: genome_vcf
     tuple val(meta), path("*genome.vcf.gz.tbi"),   emit: genome_vcf_tbi
-    path "versions.yml",                           emit: versions
+    tuple val("${task.process}"), val('strelka'), eval("configureStrelkaGermlineWorkflow.py --version"), emit: versions_strelka, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,11 +42,6 @@ process STRELKA_GERMLINE {
     mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi
     mv strelka/results/variants/variants.vcf.gz     ${prefix}.variants.vcf.gz
     mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        strelka: \$( configureStrelkaGermlineWorkflow.py --version )
-    END_VERSIONS
     """
 
     stub:
@@ -56,10 +51,5 @@ process STRELKA_GERMLINE {
     touch ${prefix}.genome.vcf.gz.tbi
     echo "" | gzip > ${prefix}.variants.vcf.gz
     touch ${prefix}.variants.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        strelka: \$( configureStrelkaSomaticWorkflow.py --version )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/strelka/germline/meta.yml b/modules/nf-core/strelka/germline/meta.yml
@@ -1,6 +1,6 @@
 name: strelka_germline
-description: Strelka2 is a fast and accurate small variant caller optimized for analysis
-  of germline variation
+description: Strelka2 is a fast and accurate small variant caller optimized for
+  analysis of germline variation
 keywords:
   - variantcalling
   - germline
@@ -9,13 +9,14 @@ keywords:
   - variants
 tools:
   - strelka:
-      description: Strelka calls somatic and germline small variants from mapped sequencing
-        reads
+      description: Strelka calls somatic and germline small variants from mapped
+        sequencing reads
       homepage: https://github.com/Illumina/strelka
       documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
       tool_dev_url: https://github.com/Illumina/strelka
       doi: 10.1038/s41592-018-0051-x
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:strelka
 input:
   - - meta:
@@ -40,7 +41,8 @@ input:
         ontologies: []
     - target_bed_index:
         type: file
-        description: Index for BED file containing target regions for variant calling
+        description: Index for BED file containing target regions for variant
+          calling
         pattern: "*.{bed.tbi}"
         ontologies: []
   - fasta:
@@ -99,13 +101,29 @@ output:
           description: index file for the genome_vcf file
           pattern: "*_genome.vcf.gz.tbi"
           ontologies: []
+  versions_strelka:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - strelka:
+          type: string
+          description: The name of the tool
+      - configureStrelkaGermlineWorkflow.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
+      - strelka:
+          type: string
+          description: The name of the tool
+      - configureStrelkaGermlineWorkflow.py --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@arontommi"
 maintainers:

diff --git a/modules/nf-core/strelka/germline/tests/main.nf.test b/modules/nf-core/strelka/germline/tests/main.nf.test
@@ -33,7 +33,7 @@ nextflow_process {
                     process.out.vcf_tbi.collect { file(it[1]).getName() },
                     path(process.out.genome_vcf.get(0).get(1)).vcf.variantsMD5,
                     process.out.genome_vcf_tbi.collect { file(it[1]).getName() },
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                     ).match() }
             )
         }
@@ -70,7 +70,7 @@ nextflow_process {
                     process.out.vcf_tbi.collect { file(it[1]).getName() },
                     path(process.out.genome_vcf.get(0).get(1)).vcf.variantsMD5,
                     process.out.genome_vcf_tbi.collect { file(it[1]).getName() },
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                     ).match() }
             )
         }
@@ -98,7 +98,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 

diff --git a/modules/nf-core/strelka/germline/tests/main.nf.test.snap b/modules/nf-core/strelka/germline/tests/main.nf.test.snap
@@ -2,41 +2,6 @@
     "human - cram - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.variants.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.variants.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.genome.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.genome.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65"
-                ],
                 "genome_vcf": [
                     [
                         {
@@ -69,16 +34,20 @@
                         "test.variants.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65"
+                "versions_strelka": [
+                    [
+                        "STRELKA_GERMLINE",
+                        "strelka",
+                        "2.9.10"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-07-08T08:53:23.28237163",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
-        "timestamp": "2024-03-20T16:07:30.81195"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "human - cram": {
         "content": [
@@ -90,15 +59,21 @@
             [
                 "test.genome.vcf.gz.tbi"
             ],
-            [
-                "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65"
-            ]
+            {
+                "versions_strelka": [
+                    [
+                        "STRELKA_GERMLINE",
+                        "strelka",
+                        "2.9.10"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-07-08T08:52:36.087466651",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.3"
-        },
-        "timestamp": "2025-09-29T15:09:16.999086"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "human - cram - target": {
         "content": [
@@ -110,14 +85,20 @@
             [
                 "test.genome.vcf.gz.tbi"
             ],
-            [
-                "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65"
-            ]
+            {
+                "versions_strelka": [
+                    [
+                        "STRELKA_GERMLINE",
+                        "strelka",
+                        "2.9.10"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-07-08T08:53:17.021875762",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.3"
-        },
-        "timestamp": "2025-09-29T15:10:22.364952"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
diff --git a/modules/nf-core/strelka/somatic/environment.yml b/modules/nf-core/strelka/somatic/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=2.7.15
   - bioconda::strelka=2.9.10=h9ee0642_1
+  - conda-forge::python=2.7.15
diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf
@@ -18,7 +18,7 @@ process STRELKA_SOMATIC {
     tuple val(meta), path("*.somatic_indels.vcf.gz.tbi"), emit: vcf_indels_tbi
     tuple val(meta), path("*.somatic_snvs.vcf.gz"),       emit: vcf_snvs
     tuple val(meta), path("*.somatic_snvs.vcf.gz.tbi"),   emit: vcf_snvs_tbi
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('strelka'), eval("configureStrelkaSomaticWorkflow.py --version"), emit: versions_strelka, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -45,11 +45,6 @@ process STRELKA_SOMATIC {
     mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}.somatic_indels.vcf.gz.tbi
     mv strelka/results/variants/somatic.snvs.vcf.gz       ${prefix}.somatic_snvs.vcf.gz
     mv strelka/results/variants/somatic.snvs.vcf.gz.tbi   ${prefix}.somatic_snvs.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        strelka: \$( configureStrelkaSomaticWorkflow.py --version )
-    END_VERSIONS
     """
 
     stub:
@@ -59,10 +54,6 @@ process STRELKA_SOMATIC {
     touch ${prefix}.somatic_indels.vcf.gz.tbi
     echo "" | gzip > ${prefix}.somatic_snvs.vcf.gz
     touch ${prefix}.somatic_snvs.vcf.gz.tbi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        strelka: \$( configureStrelkaSomaticWorkflow.py --version )
-    END_VERSIONS
     """
 }
+}
diff --git a/modules/nf-core/strelka/somatic/meta.yml b/modules/nf-core/strelka/somatic/meta.yml
@@ -1,7 +1,7 @@
 name: strelka_somatic
-description: Strelka2 is a fast and accurate small variant caller optimized for analysis
-  of germline variation in small cohorts and somatic variation in tumor/normal sample
-  pairs
+description: Strelka2 is a fast and accurate small variant caller optimized for
+  analysis of germline variation in small cohorts and somatic variation in
+  tumor/normal sample pairs
 keywords:
   - variant calling
   - germline
@@ -10,13 +10,14 @@ keywords:
   - variants
 tools:
   - strelka:
-      description: Strelka calls somatic and germline small variants from mapped sequencing
-        reads
+      description: Strelka calls somatic and germline small variants from mapped
+        sequencing reads
       homepage: https://github.com/Illumina/strelka
       documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
       tool_dev_url: https://github.com/Illumina/strelka
       doi: 10.1038/s41592-018-0051-x
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:strelka
 input:
   - - meta:
@@ -61,7 +62,8 @@ input:
         ontologies: []
     - target_bed_index:
         type: file
-        description: Index for BED file containing target regions for variant calling
+        description: Index for BED file containing target regions for variant
+          calling
         pattern: "*.{bed.tbi}"
         ontologies: []
   - fasta:
@@ -119,13 +121,29 @@ output:
           description: Index for gzipped VCF file containing variants
           pattern: "*.{vcf.gz.tbi}"
           ontologies: []
+  versions_strelka:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - strelka:
+          type: string
+          description: The name of the tool
+      - configureStrelkaSomaticWorkflow.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
+      - strelka:
+          type: string
+          description: The name of the tool
+      - configureStrelkaSomaticWorkflow.py --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
 maintainers: