feat: gridss/annotate nf-core module

modules/nf-core/gridss/annotate/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gridss=2.13.2

modules/nf-core/gridss/annotate/main.nf

@@ -0,0 +1,42 @@
+process GRIDSS_ANNOTATE {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h270b39a_0'
+        : 'biocontainers/gridss:2.13.2--h270b39a_0'}"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    tuple val("${task.process}"), val('gridss'), eval("GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}.annotated"
+    if ("${vcf}" == "${prefix}.vcf.gz") {
+        error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
+    }
+    """
+    mkdir -p ${prefix}_work
+
+    gridss_annotate_vcf_repeatmasker \\
+        --output ${prefix}.vcf.gz \\
+        --workingdir ${prefix}_work \\
+        --threads ${task.cpus} \\
+        ${args} \\
+        ${vcf}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}.annotated"
+    """
+    echo "" | gzip > ${prefix}.vcf.gz
+    """
+}

modules/nf-core/gridss/annotate/meta.yml

@@ -0,0 +1,69 @@
+name: "gridss_annotate"
+description: Annotates single breakends in a GRIDSS VCF with RepeatMasker
+  annotations using gridss_annotate_vcf_repeatmasker.
+keywords:
+  - gridss
+  - structural variants
+  - annotation
+  - repeatmasker
+  - vcf
+tools:
+  - gridss:
+      description: "GRIDSS: the Genomic Rearrangement IDentification Software Suite"
+      documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation"
+      tool_dev_url: "https://github.com/PapenfussLab/gridss"
+      doi: "10.1186/s13059-021-02423-x"
+      licence:
+        - "GPL v3"
+      identifier: biotools:gridss
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test']
+    - vcf:
+        type: file
+        description: Input VCF file generated with GRIDSS
+        pattern: "*.{vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test']
+      - "*.vcf.gz":
+          type: file
+          description: Annotated VCF file compressed with bgzip
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016"
+            - edam: http://edamontology.org/format_3989
+  versions_gridss:
+    - - ${task.process}:
+          type: string
+          description: The process
+      - gridss:
+          type: string
+          description: The tool name
+      - GeneratePonBedpe --version 2>&1 | sed 's/-gridss//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process
+      - gridss:
+          type: string
+          description: The tool name
+      - GeneratePonBedpe --version 2>&1 | sed 's/-gridss//':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@emmcauley"
+maintainers:
+  - "@emmcauley"

modules/nf-core/gridss/annotate/tests/main.nf.test

@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process GRIDSS_ANNOTATE"
+    script "../main.nf"
+    process "GRIDSS_ANNOTATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gridss"
+    tag "gridss/annotate"
+
+    test("human - vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("human - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/gridss/annotate/tests/main.nf.test.snap

@@ -0,0 +1,54 @@
+{
+    "human - vcf": {
+        "content": [
+            {
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.annotated.vcf.gz:md5,15ceb389949b96123975b0dfd7059ef3"
+                    ]
+                ],
+                "versions_gridss": [
+                    [
+                        "GRIDSS_ANNOTATE",
+                        "gridss",
+                        "2.13.2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-04-08T11:09:23.605669"
+    },
+    "human - vcf - stub": {
+        "content": [
+            {
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions_gridss": [
+                    [
+                        "GRIDSS_ANNOTATE",
+                        "gridss",
+                        "2.13.2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-04-08T11:09:54.107154"
+    }
+}

modules/nf-core/gridss/generateponbedpe/main.nf

@@ -16,7 +16,7 @@ process GRIDSS_GENERATEPONBEDPE {
     output:
     tuple val(meta), path("*.bedpe"), emit: bedpe
     tuple val(meta), path("*.bed"), emit: bed
-    tuple val("${task.process}"), val('gridss'), eval("echo \$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
+    tuple val("${task.process}"), val('gridss'), eval("GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/gridss/generateponbedpe/meta.yml

@@ -96,18 +96,18 @@ output:
       - gridss:
           type: string
           description: The tool name
-      - "echo \\$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//'":
+      - GeneratePonBedpe --version 2>&1 | sed 's/-gridss//':
           type: eval
-          description: The command used to generate the version of the tool
+          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
           type: string
-          description: The name of the process
+          description: The process
       - gridss:
           type: string
-          description: The name of the tool
-      - echo \$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//':
+          description: The tool name
+      - GeneratePonBedpe --version 2>&1 | sed 's/-gridss//':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

modules/nf-core/gridss/generateponbedpe/tests/main.nf.test.snap

@@ -15,9 +15,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T10:46:06.531660941"
+        "timestamp": "2026-04-08T10:41:23.697519"
     },
     "human - vcf - stub": {
         "content": [
@@ -72,8 +72,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T10:46:26.933625676"
+        "timestamp": "2026-04-08T10:42:09.002776"
     }
 }

modules/nf-core/gridss/gridss/main.nf

@@ -15,7 +15,7 @@ process GRIDSS_GRIDSS {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    tuple val("${task.process}"), val('gridss'), eval("echo \$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
+    tuple val("${task.process}"), val('gridss'), eval("GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/gridss/gridss/meta.yml

@@ -73,9 +73,9 @@ output:
       - gridss:
           type: string
           description: The tool name
-      - "echo \\$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//'":
+      - GeneratePonBedpe --version 2>&1 | sed 's/-gridss//':
           type: eval
-          description: The command used to generate the version of the tool
+          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
@@ -84,9 +84,9 @@ topics:
       - gridss:
           type: string
           description: The tool name
-      - "echo \\$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//'":
+      - GeneratePonBedpe --version 2>&1 | sed 's/-gridss//':
           type: eval
-          description: The command used to generate the version of the tool
+          description: The expression to obtain the version of the tool
 authors:
   - "@nvnieuwk"
 maintainers:

modules/nf-core/gridss/gridss/tests/main.nf.test.snap

@@ -36,9 +36,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T10:48:07.535353275"
+        "timestamp": "2026-04-08T14:42:13.099952"
     },
     "human - bam - bwa": {
         "content": [
@@ -55,9 +55,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T10:46:57.020256457"
+        "timestamp": "2026-04-08T14:39:51.733509"
     },
     "human - bam": {
         "content": [
@@ -74,9 +74,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T10:47:25.316078382"
+        "timestamp": "2026-04-08T14:40:47.897835"
     },
     "human - cram": {
         "content": [
@@ -93,8 +93,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T10:47:55.929740389"
+        "timestamp": "2026-04-08T14:41:44.192114"
     }
 }

modules/nf-core/gridss/somaticfilter/main.nf

@@ -14,7 +14,7 @@ process GRIDSS_SOMATICFILTER {
     output:
     tuple val(meta), path("*.high_confidence_somatic.vcf.bgz"), emit: high_conf_sv
     tuple val(meta), path("*.all_somatic.vcf.bgz"), emit: all_sv
-    tuple val("${task.process}"), val('gridss'), eval("echo \$(GeneratePonBedpe --version 2>&1) | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
+    tuple val("${task.process}"), val('gridss'), eval("GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'"), topic: versions, emit: versions_gridss
 
     when:
     task.ext.when == null || task.ext.when