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8bc5236371
* Created hmmer/eslalimask from template * esl-alimask module with --rf-is-mask test case * Add optional file output * Add hmmer to test name * Move from process_single to process_low * Test for versions.yml, plus content * Prettier * Avoid gzipping input alignment * hmmer/eslreformat from template * Started on main.nf * meta.id to prefix * Continued work * Fix version string so it's from *this* tool * hmmer/eslreformat * Prettier * Get tests/config/pytest_modules.yml back * Delete extra hmmer/eslalimask in pytest_modules.yml * More prettier * Fix path to versions.yml in test * Remove 'format' param * Fix problems with format param deletion * Document format param
36 lines
1 KiB
Text
36 lines
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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"""
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esl-reformat \\
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-o ${prefix}.sequences \\
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$args \\
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$seqfile
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gzip ${prefix}.sequences
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cat <<-END_VERSIONS > versions.yml
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"${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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