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https://github.com/MillironX/nf-core_modules.git
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43 lines
1.2 KiB
Text
43 lines
1.2 KiB
Text
process SRATOOLS_PREFETCH {
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tag "$id"
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label 'process_low'
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label 'error_retry'
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conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
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'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
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input:
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tuple val(meta), val(id)
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output:
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tuple val(meta), path("$id"), emit: sra
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
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"""
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eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
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if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
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mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
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printf '${config}' > "\${NCBI_SETTINGS}"
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fi
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prefetch \\
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$args \\
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--progress \\
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$id
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vdb-validate $id
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
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END_VERSIONS
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"""
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}
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