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885e724e07
* Add postprocessing option to hmmer/eslreformat * Update tests/modules/hmmer/eslreformat/nextflow.config Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/hmmer/eslreformat/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
process HMMER_ESLREFORMAT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1':
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'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }"
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input:
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tuple val(meta), path(seqfile)
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output:
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tuple val(meta), path("*.sequences.gz"), emit: seqreformated
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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 ?: "${meta.id}"
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// Use for any postprocessing of the sequence file, e.g. removal of gap characters
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def postproc = task.ext.postprocessing ?: ""
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"""
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esl-reformat \\
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$args \\
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$seqfile \\
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$postproc \\
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| gzip -c > ${prefix}.sequences.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmmer/easel: \$(esl-reformat -h | grep -o '^# Easel [0-9.]*' | sed 's/^# Easel *//')
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END_VERSIONS
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"""
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}
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