mirror of
https://github.com/MillironX/nf-core_modules.git
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57 lines
2.2 KiB
Text
57 lines
2.2 KiB
Text
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process HMMER_ESLALIMASK {
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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(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all)
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path maskfile
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output:
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tuple val(meta), path("*.masked.sthlm.gz"), emit: maskedaln
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path "*.fmask-rf.gz" , emit: fmask_rf , optional: true
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path "*.fmask-all.gz" , emit: fmask_all, optional: true
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path "*.gmask-rf.gz" , emit: gmask_rf , optional: true
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path "*.gmask-all.gz" , emit: gmask_all, optional: true
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path "*.pmask-rf.gz" , emit: pmask_rf , optional: true
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path "*.pmask-all.gz" , emit: pmask_all, optional: true
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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 fmask_rfarg = fmask_rf ? "--fmask-rf ${prefix}.fmask-rf" : ""
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def fmask_allarg = fmask_all ? "--fmask-all ${prefix}.fmask-all" : ""
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def gmask_rfarg = gmask_rf ? "--gmask-rf ${prefix}.gmask-rf" : ""
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def gmask_allarg = gmask_all ? "--gmask-all ${prefix}.gmask-all" : ""
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def pmask_rfarg = pmask_rf ? "--pmask-rf ${prefix}.pmask-rf" : ""
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def pmask_allarg = pmask_all ? "--pmask-all ${prefix}.pmask-all" : ""
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"""
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esl-alimask \\
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$args \\
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$fmask_rfarg \\
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$fmask_allarg \\
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$gmask_rfarg \\
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$gmask_allarg \\
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$pmask_rfarg \\
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$pmask_allarg \\
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-o ${prefix}.masked.sthlm \\
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$unmaskedaln \\
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$maskfile
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gzip ${prefix}.*mask*
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cat <<-END_VERSIONS > versions.yml
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"${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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