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4f78d40b11
* New module for fasta_windows
* Upgraded the code and the test to v2.4
* Standard list of Fasta file extensions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Output file (and/or directory) names SHOULD just consist of only ${prefix}
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
process FASTAWINDOWS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::fasta_windows=0.2.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0':
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'quay.io/biocontainers/fasta_windows:0.2.4--hec16e2b_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("fw_out/*_freq_windows.tsv") , emit: freq
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tuple val(meta), path("fw_out/*_mononuc_windows.tsv") , emit: mononuc
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tuple val(meta), path("fw_out/*_dinuc_windows.tsv") , emit: dinuc
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tuple val(meta), path("fw_out/*_trinuc_windows.tsv") , emit: trinuc
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tuple val(meta), path("fw_out/*_tetranuc_windows.tsv"), emit: tetranuc
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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rm -rf fw_out
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env RAYON_NUM_THREADS=$task.cpus \\
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fasta_windows \\
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$args \\
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--fasta $fasta \\
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--output ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fasta_windows: \$(fasta_windows --version | cut -d' ' -f3)
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END_VERSIONS
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"""
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}
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