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794f84534b
* 📦 NEW: Add gstama/polyacleanup polyacleanup script remove remaining polyA tails from FLNC reads (Pacbio isoseq3) * 🐛 FIX: Prettier: replace simple quote by double quote * 🐛 FIX: Update TEMPLATE to nf-core 2.4 * 👌 IMPROVE: Compress outputs Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
40 lines
1.4 KiB
Text
40 lines
1.4 KiB
Text
process GSTAMA_POLYACLEANUP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0':
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'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*_tama.fa.gz") , emit: fasta
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tuple val(meta), path("*_tama_polya_flnc_report.txt.gz"), emit: report
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tuple val(meta), path("*_tama_tails.fa.gz") , emit: tails
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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 ?: "${meta.id}"
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if( "$fasta" == "${prefix}.fasta" | "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, set prefix in module configuration"
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"""
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tama_flnc_polya_cleanup.py \\
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-f $fasta \\
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-p ${prefix} \\
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$args
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gzip ${prefix}.fa
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gzip ${prefix}_polya_flnc_report.txt
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gzip ${prefix}_tails.fa
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
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END_VERSIONS
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"""
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}
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