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48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
process SRATOOLS_FASTERQDUMP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
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'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
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input:
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tuple val(meta), path(sra)
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path ncbi_settings
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output:
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tuple val(meta), path(output), emit: reads
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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 args2 = task.ext.args2 ?: ''
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// Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
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// *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
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// for unpaired reads which we ignore here.
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output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
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"""
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export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
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fasterq-dump \\
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$args \\
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--threads $task.cpus \\
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${sra.name}
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pigz \\
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$args2 \\
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--no-name \\
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--processes $task.cpus \\
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*.fastq
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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