Merge branch 'master' into stub-topics-smoothxg

Author: HReed1

modules/nf-core/annotsv/annotsv/main.nf

@@ -18,8 +18,8 @@ process ANNOTSV_ANNOTSV {
     tuple val(meta5), path(gene_transcripts)
 
     output:
-    tuple val(meta), path("*.tsv")            , emit: tsv
-    tuple val(meta), path("*.unannotated.tsv"), emit: unannotated_tsv, optional: true
+    tuple val(meta), path("${prefix}.tsv")            , emit: tsv
+    tuple val(meta), path("${prefix}.unannotated.tsv"), emit: unannotated_tsv, optional: true
     tuple val(meta), path("*.vcf")            , emit: vcf            , optional: true
     tuple val("${task.process}"), val('annotsv'), eval("AnnotSV --version | sed 's/AnnotSV //'"), emit: versions_annotsv, topic: versions
 
@@ -28,7 +28,7 @@ process ANNOTSV_ANNOTSV {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     def cand_genes     = candidate_genes          ? "-candidateGenesFile ${candidate_genes}"              : ""
     def small_variants = candidate_small_variants ? "-candidateSnvIndelFiles ${candidate_small_variants}" : ""
@@ -51,7 +51,7 @@ process ANNOTSV_ANNOTSV {
 
     stub:
     def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     def create_vcf = args.contains("-vcf 1") ? "touch ${prefix}.vcf" : ""
 

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

@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "annotsv_annotsv"
 description: Annotation and Ranking of Structural Variation
 keywords:
@@ -91,7 +92,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.tsv":
+      - "${prefix}.tsv":
           type: file
           description: A TSV file containing the annotated variants
           pattern: "*.tsv"
@@ -103,7 +104,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.unannotated.tsv":
+      - "${prefix}.unannotated.tsv":
           type: file
           description: OPTIONAL - TSV file containing the unannotated variants
           pattern: "*.unannotated.tsv"

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

@@ -7,10 +7,7 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.unannotated.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "unannotated_tsv": [
@@ -38,10 +35,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-11T16:06:19.47501651",
+        "timestamp": "2026-05-01T10:39:49.368087494",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.2"
         }
     }
 }

modules/nf-core/bio2zarr/vcf2zarrconvert/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::bio2zarr=0.1.8"

modules/nf-core/bio2zarr/vcf2zarrconvert/main.nf

@@ -0,0 +1,40 @@
+process BIO2ZARR_VCF2ZARRCONVERT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/77/7713d869c8c8259c10701c95fc105bad8bcfbd6735de6941a47c9e6e26e9bb2f/data':
+        'community.wave.seqera.io/library/bio2zarr:0.1.8--c2c92dd3f64fb0f9' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.vcz"), emit: vcz
+    tuple val("${task.process}"), val('vcf2zarr'), eval('vcf2zarr --version |& sed -n "s/.* //p"'), topic: versions  , emit: versions_vcf2zarr
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    vcf2zarr \\
+        convert \\
+        ${args} \\
+        --worker-processes ${task.cpus} \\
+        ${vcf} \\
+        ${prefix}.vcz
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    mkdir ${prefix}.vcz
+    """
+}

modules/nf-core/bio2zarr/vcf2zarrconvert/meta.yml

@@ -0,0 +1,67 @@
+name: "bio2zarr_vcf2zarrconvert"
+description: Convert VCF data to the VCF Zarr specification reliably, in parallel or distributed over a cluster.
+keywords:
+  - vcf
+  - zarr
+  - convert
+  - genomics
+tools:
+  - "vcf2zarr":
+      description: "Convert bioinformatics data to Zarr"
+      homepage: "https://sgkit-dev.github.io/bio2zarr/vcf2zarr/overview.html"
+      documentation: "https://sgkit-dev.github.io/bio2zarr/"
+      tool_dev_url: "https://github.com/sgkit-dev/bio2zarr"
+      doi: "10.1101/2024.06.11.598241"
+      licence:
+        - "Apache-2.0"
+      identifier: biotools:bio2zarr
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - vcf:
+        type: file
+        description: Input VCF/BCF file to convert
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016" # VCF
+          - edam: "http://edamontology.org/format_3020" # BCF
+output:
+  vcz:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.vcz":
+          type: directory
+          description: Output VCF Zarr store directory
+          pattern: "*.vcz"
+          ontologies: []
+  versions_vcf2zarr:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - vcf2zarr:
+          type: string
+          description: The name of the tool
+      - vcf2zarr --version |& sed -n "s/.* //p":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - vcf2zarr:
+          type: string
+          description: The name of the tool
+      - vcf2zarr --version |& sed -n "s/.* //p":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@camlloyd"
+maintainers:
+  - "@camlloyd"

modules/nf-core/bio2zarr/vcf2zarrconvert/tests/main.nf.test

@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process BIO2ZARR_VCF2ZARRCONVERT"
+    script "../main.nf"
+    process "BIO2ZARR_VCF2ZARRCONVERT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bio2zarr"
+    tag "bio2zarr/vcf2zarrconvert"
+
+    test("sarscov2 - vcf.gz - vcz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - vcf.gz - vcz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}