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42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process LAST_LASTAL {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::last=1250' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
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'quay.io/biocontainers/last:1250--h2e03b76_0' }"
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input:
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tuple val(meta), path(fastx), path (param_file)
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path index
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output:
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tuple val(meta), path("*.maf.gz"), emit: maf
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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 trained_params = param_file ? "-p ${param_file}" : ''
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"""
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INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
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lastal \\
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$trained_params \\
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$args \\
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-P $task.cpus \\
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${index}/\$INDEX_NAME \\
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$fastx \\
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| gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz
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# gzip needs --no-name otherwise it puts a timestamp in the file,
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# which makes its checksum non-reproducible.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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last: \$(lastal --version 2>&1 | sed 's/lastal //')
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END_VERSIONS
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"""
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}
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