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0857e6c60f
* Adding gappa/examineheattree * Update modules/gappa/examineheattree/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Check versions.yml for md5 sum instead Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
process GAPPA_EXAMINEHEATTREE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0':
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'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }"
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input:
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tuple val(meta), path(jplace)
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output:
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tuple val(meta), path("*.newick") , emit: newick , optional: true
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tuple val(meta), path("*.nexus") , emit: nexus , optional: true
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tuple val(meta), path("*.phyloxml") , emit: phyloxml, optional: true
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tuple val(meta), path("*.svg") , emit: svg , optional: true
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tuple val(meta), path("*.colours.txt"), emit: colours
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tuple val(meta), path("*.log") , emit: log
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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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gappa \\
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examine \\
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heat-tree \\
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--threads $task.cpus \\
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--file-prefix ${prefix}. \\
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--jplace-path $jplace \\
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$args \\
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--log-file ${prefix}.log
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grep '^ *At' ${prefix}.log > ${prefix}.colours.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
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END_VERSIONS
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"""
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}
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