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New module: regtools junction extract (#7033)
* initial commit * Update modules/nf-core/regtools/junctionsextract/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/regtools/junctionsextract/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/regtools/junctionsextract/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * more recent fill file path * Update modules/nf-core/regtools/junctionsextract/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/regtools/junctionsextract/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/regtools/junctionsextract/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * update snapshot to include out not out.junc * Update modules/nf-core/regtools/junctionsextract/environment.yml Co-authored-by: Edmund Miller <[email protected]> * Update modules/nf-core/regtools/junctionsextract/main.nf Co-authored-by: Edmund Miller <[email protected]> * Update modules/nf-core/regtools/junctionsextract/main.nf Co-authored-by: Edmund Miller <[email protected]> * fix meta.yml * test: Add versions check * fix: Update regtools version extraction regex in junctionsextract module --------- Co-authored-by: Lorena Pantano <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Edmund Miller <[email protected]>
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‎modules/nf-core/regtools/junctionsextract/environment.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::regtools=0.5.0"

‎modules/nf-core/regtools/junctionsextract/main.nf‎

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process REGTOOLS_JUNCTIONSEXTRACT {
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tag "$meta.id"
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label 'process_low'
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conda "bioconda::regtools=0.5.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b6c0653189b95b22e16038f61ade205a865857f54eeae9ba0184490a1834f7c9/data' :
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'community.wave.seqera.io/library/regtools:0.5.0--b9a260c4c898354a' }"
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("*.junc"), emit: junc
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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regtools junctions extract \\
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$args \\
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-o ${prefix}.junc \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.junc
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
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END_VERSIONS
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"""
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}

‎modules/nf-core/regtools/junctionsextract/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "regtools_junctionsextract"
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description: Extract exon-exon junctions from an RNAseq BAM file. The output is a
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BED file in the BED12 format.
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keywords:
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- regtools
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- leafcutter
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- RNA-seq
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- splicing
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tools:
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- "regtools":
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description: "RegTools is a set of tools that integrate DNA-seq and RNA-seq data
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to help interpret mutations in a regulatory and splicing context."
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homepage: "https://regtools.readthedocs.io/en/latest/"
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documentation: "https://regtools.readthedocs.io/en/latest/#usage"
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tool_dev_url: "https://github.com/griffithlab/regtools"
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licence: ["MIT"]
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identifier: biotools:regtools
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- bam:
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type: file
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description: Sorted BAM file
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pattern: "*.{bam}"
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- bai:
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type: file
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description: Index to sorted BAM file
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pattern: "*.{bai}"
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output:
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- junc:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- "*.junc":
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type: file
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description: |
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BED12 file containing exon-exon "regtools_junctionsextract"
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pattern: "*.{junc}"
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- versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@abartlett004"
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maintainers:
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- "@abartlett004"

‎modules/nf-core/regtools/junctionsextract/tests/main.nf.test‎

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nextflow_process {
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name "Test Process REGTOOLS_JUNCTIONSEXTRACT"
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script "../main.nf"
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process "REGTOOLS_JUNCTIONSEXTRACT"
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tag "modules"
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tag "modules_nfcore"
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tag "regtools"
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tag "regtools/junctionsextract"
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test("homo_sapiens - bam-bai") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test', single_end:false ], // meta map
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo_sapiens - bam-bai - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test', single_end:false ], // meta map
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
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file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() },
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{ assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }
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)
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}
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}
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}

‎modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap‎

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{
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"homo_sapiens - bam-bai - stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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"versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
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],
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"junc": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions": [
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"versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.1"
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},
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"timestamp": "2024-11-20T13:29:27.373772"
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},
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"versions": {
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"content": [
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{
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"REGTOOLS_JUNCTIONSEXTRACT": {
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"regtools": "0.5.0"
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}
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.1"
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},
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"timestamp": "2024-11-20T13:29:27.448238"
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},
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"homo_sapiens - bam-bai": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
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]
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],
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"1": [
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"versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
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],
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"junc": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
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]
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],
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"versions": [
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"versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.1"
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},
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"timestamp": "2024-11-20T13:29:23.165022"
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}
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}

‎modules/nf-core/regtools/junctionsextract/tests/tags.yml‎

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regtools/junctionsextract:
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- "modules/nf-core/regtools/junctionsextract/**"

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