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0d53a34eed
* initiate agrvate module * remove todos [ci skip] * initiate fastani draft [ci skip] * clean stubs [ci skip] * interim commit [ci skip] * accomodate the batch/per-sample processing [ci skip] * use the meta map [ci skip] * run first test [ci skip] * remove extra spaces [ci skip] * change output file name [ci skip] * update the expected output [ci skip] * update the files used for test [ci skip] * fix typo [ci skip] * test passing [ci skip] * update the description * remove extra files * accomodate CR suggestions [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * accomodate CR suggestions [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * accomodate CR suggestions [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * use meta map for batch analysis * fix the tests * rely upon tuples * Apply suggestions from code review * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
52 lines
1.6 KiB
Text
52 lines
1.6 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 FASTANI {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::fastani=1.32" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0"
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} else {
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container "quay.io/biocontainers/fastani:1.32--he1c1bb9_0"
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}
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input:
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tuple val(meta), path(query)
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path reference
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output:
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tuple val(meta), path("*.ani.txt"), emit: ani
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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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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (meta.batch_input) {
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"""
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fastANI \\
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-ql $query \\
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-rl $reference \\
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-o ${prefix}.ani.txt
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echo \$(fastANI --version 2>&1) | sed 's/version//;' > ${software}.version.txt
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"""
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} else {
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"""
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fastANI \\
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-q $query \\
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-r $reference \\
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-o ${prefix}.ani.txt
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echo \$(fastANI --version 2>&1) | sed 's/version//;' > ${software}.version.txt
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"""
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}
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}
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