Pbsv/call

modules/nf-core/pbsv/call/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::pbsv=2.9.0"

modules/nf-core/pbsv/call/main.nf

@@ -0,0 +1,44 @@
+process PBSV_CALL {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0':
+        'biocontainers/pbsv:2.9.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta),  path(svsig)
+    tuple val(meta2), path(fasta)
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //')
+    END_VERSIONS
+    """
+}

modules/nf-core/pbsv/call/meta.yml

@@ -0,0 +1,50 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pbsv_call"
+description: "pbsv/call - PacBio structural variant (SV) calling and analysis tools"
+keywords:
+  - variant
+  - pacbio
+  - genomics
+tools:
+  - "pbsv":
+      description: "pbsv - PacBio structural variant (SV) calling and analysis tools"
+      homepage: "https://github.com/PacificBiosciences/"
+      documentation: "https://github.com/PacificBiosciences/"
+      tool_dev_url: "https://github.com/PacificBiosciences/"
+      licence: ["BSD-3-clause-Clear"]
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - svsig:
+        type: file
+        description: structural variant file
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'reference']`
+    - fasta:
+        type: file
+        description: fasta file used as reference
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.vcf":
+          type: file
+          description: structural variant file
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@tanyasarkjain"
+maintainers:
+  - "@tanyasarkjain"

modules/nf-core/pbsv/call/tests/main.nf.test

@@ -0,0 +1,68 @@
+nextflow_process {
+    name "Test Process PBSV_CALL"
+    script "../main.nf"
+    process "PBSV_CALL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbsv"
+    tag "pbsv/call"
+
+    test("pbsv-call - [svsig] [fasta]") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path +  'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            def vcfFile = path(process.out.vcf[0][1]).vcf
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.vcf[0][1]).name,
+                    process.out.versions,
+                    vcfFile.variantsMD5).match() },
+                { assert vcfFile.chromosomes == ['chr19:45760000-45770300'] as Set}
+            )
+        }
+    }
+
+    test("pbsv-call - [svsig] [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path +  'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/pbsv/call/tests/main.nf.test.snap

@@ -0,0 +1,52 @@
+{
+    "pbsv-call - [svsig] [fasta]": {
+        "content": [
+
+            "test.vcf",
+            [
+                "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b"
+            ],
+            "39821c95936a6f9539d3ad53e6562f99"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T16:50:00.253251"
+    },
+    "pbsv-call - [svsig] [fasta] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T21:38:47.484071"
+    }
+}