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https://github.com/MillironX/nf-core_modules.git
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07c0830057
* chore: apply module template * refactor: add NCBI settings to options * docs: complete meta information * feat: add prefetch process * fix: correct bash commands * tests: define the right tests * style: move option definition to satisfy linting * fix: extract version correctly * fix: correct newline issues * refactor: address review comments * Apply suggestions from code review * chore: add retrying via nf-core label * refactor: validate download thoroughly * refactor: remove vdb-config input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
1.6 KiB
Text
50 lines
1.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SRATOOLS_PREFETCH {
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tag "$id"
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label 'process_low'
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label 'error_retry'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0'
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} else {
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container 'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0'
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}
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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("$id"), emit: sra
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path "versions.yml" , emit: versions
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script:
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def config = "/LIBS/GUID = \"${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 '${config}' > "\${NCBI_SETTINGS}"
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fi
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prefetch \\
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$options.args \\
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--progress \\
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$id
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vdb-validate $id
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(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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