55 lines
1.5 KiB
Text
Generated
55 lines
1.5 KiB
Text
Generated
process MULTIQC {
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
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'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
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input:
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path multiqc_files, stageAs: "?/*"
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path(multiqc_config)
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path(extra_multiqc_config)
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path(multiqc_logo)
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output:
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path "*multiqc_report.html", emit: report
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path "*_data" , emit: data
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path "*_plots" , optional:true, emit: plots
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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 = multiqc_config ? "--config $multiqc_config" : ''
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def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
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def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
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"""
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multiqc \\
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--force \\
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$args \\
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$config \\
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$extra_config \\
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$logo \\
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.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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END_VERSIONS
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"""
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stub:
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"""
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mkdir multiqc_data
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touch multiqc_plots
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touch multiqc_report.html
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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END_VERSIONS
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"""
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}
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