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https://github.com/MillironX/nf-core_modules.git
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a69faefee8
* Added seqtk/rename module and tests code * Updated files and testing code for seqtk rename * Added meta map to seqtk/rename module def * updated prefix parameter usage * updated test.yml to remove local filepaths --> change to output * Added empty line to main.nf
40 lines
1.1 KiB
Text
40 lines
1.1 KiB
Text
process SEQTK_RENAME {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
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'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
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input:
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tuple val(meta), path(sequences)
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output:
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tuple val(meta), path("*.gz") , emit: sequences
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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 ?: "${meta.id}"
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def extension = "fasta"
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if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
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extension = "fastq"
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}
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"""
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seqtk \\
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rename \\
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$args \\
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$sequences \\
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$prefix | \\
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gzip -c --no-name > ${prefix}.renamed.${extension}.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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