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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
48 lines
1.5 KiB
Text
48 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 QUAST {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
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} else {
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container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
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}
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input:
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path consensus
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path fasta
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path gff
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val use_fasta
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val use_gff
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output:
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path "${prefix}" , emit: results
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path '*.tsv' , emit: tsv
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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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prefix = options.suffix ?: software
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def features = use_gff ? "--features $gff" : ''
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def reference = use_fasta ? "-r $fasta" : ''
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"""
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quast.py \\
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--output-dir $prefix \\
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$reference \\
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$features \\
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--threads $task.cpus \\
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$options.args \\
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${consensus.join(' ')}
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ln -s ${prefix}/report.tsv
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echo \$(quast.py --version 2>&1) | sed 's/^.*QUAST v//; s/ .*\$//' > ${software}.version.txt
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"""
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}
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