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36 lines
1 KiB
Text
36 lines
1 KiB
Text
process FFQ {
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tag "${ids.size() == 1 ? ids[0] : "${ids[0]+'..'+ids[-1]}"}"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::ffq=0.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ffq:0.2.1--pyhdfd78af_0':
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'quay.io/biocontainers/ffq:0.2.1--pyhdfd78af_0' }"
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input:
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val ids
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output:
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path "*.json" , emit: json
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def id_list = ids.sort()
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def name = id_list.size() == 1 ? ids[0] : 'metadata'
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def prefix = task.ext.prefix ?: "${name}"
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"""
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ffq \\
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${id_list.join(' ')} \\
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$args \\
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> ${prefix}.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ffq: \$(echo \$(ffq --help 2>&1) | sed 's/^.*ffq //; s/: A command.*\$//' )
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END_VERSIONS
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"""
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}
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