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1d668eefa2
* Update seqwish to version 0.7.2 * seqwish can work with a comma-separated list of PAFs * level with nf-core/modules master branch * update seqwish/induce to v0.7.6 * add pangenome test data * test seqwish/induce v0.7.6 with pangenomics test data * we already have pointed to the pangenomics test data sets * update paths to test data * add path to bgzipped fa, gzi, fai * remove one tab * remove one tab * actually execute the 2nd test * try to fix versions.yml * pangenomic tests can be run in their own subworkflow * maybe the csv input is the problem * remove space as suggested by Rike * csv input was not the problem * update test.yml * typo * enable pangenome tests * add md5sum for pangenomic test * Update tests/modules/seqwish/induce/test.yml Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * PAF input is a list of files * beautify comment Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
process SEQWISH_INDUCE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' :
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'quay.io/biocontainers/seqwish:0.7.6--h5b5514e_1' }"
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input:
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tuple val(meta), path(paf), path(fasta)
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output:
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tuple val(meta), path("*.gfa"), emit: gfa
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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 input = paf.join(',') // this ensures that we can actually input a
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// comma-separated list of PAF files as required by
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// https://github.com/nf-core/pangenome. If one wants to use this,
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// ensure that you put a ".collect()" behind your channel.
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// See https://github.com/nf-core/pangenome/blob/34149c6cdc19bce3a7b99f97c769d8986a8d429b/main.nf#L543
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// for an example.
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"""
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seqwish \\
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--threads $task.cpus \\
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--paf-alns=$input \\
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--seqs=$fasta \\
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--gfa=${prefix}.gfa \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seqwish: \$(echo \$(seqwish --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v')
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END_VERSIONS
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"""
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}
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