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41 lines
1.5 KiB
Text
41 lines
1.5 KiB
Text
process RAPIDNJ {
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label 'process_medium'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' :
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'quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' }"
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input:
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path alignment
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output:
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path "*.sth" , emit: stockholm_alignment
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path "*.tre" , emit: phylogeny
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def VERSION = '2.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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python \\
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-c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'
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rapidnj \\
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alignment.sth \\
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$args \\
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-i sth \\
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-c $task.cpus \\
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-x rapidnj_phylogeny.tre
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rapidnj: $VERSION
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biopython: \$(python -c "import Bio; print(Bio.__version__)")
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END_VERSIONS
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"""
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}
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