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https://github.com/MillironX/nf-core_modules.git
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a0443e2c54
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier * Fix incorrect quotes in tags Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
44 lines
1.2 KiB
Text
44 lines
1.2 KiB
Text
process HMMER_HMMBUILD {
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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--h87f3376_2':
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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(alignment)
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path mxfile
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output:
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tuple val(meta), path("*.hmm.gz"), emit: hmm
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path "*.hmmbuild.txt", emit: hmmbuildout
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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 mxfileopt = mxfile ? "--mxfile ${mxfile}" : ""
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"""
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hmmbuild \\
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$args \\
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--cpu $task.cpus \\
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-n ${prefix} \\
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-o ${prefix}.hmmbuild.txt \\
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${mxfileopt} \\
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${prefix}.hmm \\
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$alignment
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gzip ${prefix}.hmm
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1))
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END_VERSIONS
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"""
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}
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