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37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
process HMMER_HMMALIGN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
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container "${ 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(fasta)
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path hmm
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output:
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tuple val(meta), path("*.sthlm.gz"), emit: sthlm
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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 fastacmd = fasta.getExtension() == 'gz' ? "gunzip -c $fasta" : "cat $fasta"
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"""
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$fastacmd | \\
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hmmalign \\
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$args \\
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$hmm \\
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- | gzip -c > ${meta.id}.sthlm.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
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END_VERSIONS
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"""
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}
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