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https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process TIDDIT_SV {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0"
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} else {
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container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0"
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}
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input:
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tuple val(meta), path(bam)
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path fasta
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path fai
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output:
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tuple val(meta), path("*.vcf"), emit: vcf
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tuple val(meta), path("*.ploidy.tab"), emit: ploidy
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tuple val(meta), path("*.signals.tab"), emit: signals
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def output = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
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def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
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"""
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tiddit \\
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--sv $options.args \\
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--bam $bam \\
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$reference \\
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-o $output
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echo \$(tiddit -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
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"""
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}
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