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9764eef361
* Update eido/validate module * Update modules/eido/convert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
38 lines
1 KiB
Text
38 lines
1 KiB
Text
process EIDO_CONVERT {
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tag '$samplesheet'
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' :
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'biocontainers/eido:0.1.9_cv1' }"
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input:
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path samplesheet
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val format
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path pep_input_base_dir
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output:
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path "versions.yml" , emit: versions
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path "${prefix}.${format}" , emit: samplesheet_converted
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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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prefix = task.ext.prefix ?: "samplesheet_converted"
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"""
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eido \\
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convert \\
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-f $format \\
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$samplesheet \\
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$args \\
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-p samples=${prefix}.${format}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
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END_VERSIONS
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"""
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}
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