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* changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
68 lines
2.3 KiB
Text
68 lines
2.3 KiB
Text
process FLYE {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::flye=2.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' :
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'quay.io/biocontainers/flye:2.9--py39h6935b12_1' }"
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input:
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tuple val(meta), path(reads)
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val mode
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output:
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tuple val(meta), path("*.fasta.gz"), emit: fasta
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tuple val(meta), path("*.gfa.gz") , emit: gfa
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tuple val(meta), path("*.gv.gz") , emit: gv
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tuple val(meta), path("*.txt") , emit: txt
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tuple val(meta), path("*.log") , emit: log
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tuple val(meta), path("*.json") , emit: json
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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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def valid_mode = ["--pacbio-raw", "--pacbio-corr", "--pacbio-hifi", "--nano-raw", "--nano-corr", "--nano-hq"]
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if ( !valid_mode.contains(mode) ) { error "Unrecognised mode to run Flye. Options: ${valid_mode.join(', ')}" }
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"""
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flye \\
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$mode \\
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$reads \\
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--out-dir . \\
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--threads \\
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$task.cpus \\
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$args
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gzip -c assembly.fasta > ${prefix}.assembly.fasta.gz
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gzip -c assembly_graph.gfa > ${prefix}.assembly_graph.gfa.gz
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gzip -c assembly_graph.gv > ${prefix}.assembly_graph.gv.gz
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mv assembly_info.txt ${prefix}.assembly_info.txt
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mv flye.log ${prefix}.flye.log
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mv params.json ${prefix}.params.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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flye: \$( flye --version )
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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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echo stub > assembly.fasta | gzip -c assembly.fasta > ${prefix}.assembly.fasta.gz
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echo stub > assembly_graph.gfa | gzip -c assembly_graph.gfa > ${prefix}.assembly_graph.gfa.gz
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echo stub > assembly_graph.gv | gzip -c assembly_graph.gv > ${prefix}.assembly_graph.gv.gz
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echo contig_1 > ${prefix}.assembly_info.txt
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echo stub > ${prefix}.flye.log
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echo stub > ${prefix}.params.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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flye: \$( flye --version )
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END_VERSIONS
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"""
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}
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