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1 process MULTIQC {
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2 label 'process_micro'
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3 tag 'MultiQC'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.19" : null)
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6 conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
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9 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
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10
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11 input:
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12 path multiqc_files
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13
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14 output:
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15 path "*multiqc*"
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16 path "*multiqc_report.html", emit: report
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17 path "*_data" , emit: data
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18 path "*_plots" , emit: plots, optional: true
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19 path "versions.yml" , emit: versions
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20
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21 when:
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22 task.ext.when == null || task.ext.when
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23
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24 script:
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25 def args = task.ext.args ?: ''
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26 """
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27 cp ${params.projectconf}${params.fs}multiqc${params.fs}${params.pipeline}_mqc.yml cpipes_mqc_config.yml
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28 sed -i -e 's/Workflow_Name_Placeholder/${params.pipeline}/g; s/Workflow_Version_Placeholder/${params.workflow_version}/g' cpipes_mqc_config.yml
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29 sed -i -e 's/CPIPES_Version_Placeholder/${workflow.manifest.version}/g; s|Workflow_Output_Placeholder|${params.output}|g' cpipes_mqc_config.yml
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30 sed -i -e 's|Workflow_Input_Placeholder|${params.input}|g' cpipes_mqc_config.yml
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31
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32 if [ -n "\$(ls *filtlong.log 2> /dev/null)" ]; then
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33 sed -i -e 's%,%%g' *filtlong.log
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34 fi
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35
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36 multiqc --interactive -c cpipes_mqc_config.yml -f $args .
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37
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38 cat <<-END_VERSIONS > versions.yml
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39 "${task.process}":
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40 multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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41 END_VERSIONS
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42
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43 sedver=""
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44
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45 if [ "${workflow.containerEngine}" != "null" ]; then
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46 sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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47 else
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48 sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
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49 fi
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50
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51 cat <<-END_VERSIONS >> versions.yml
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52 sed: \$sedver
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53 END_VERSIONS
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54 """
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55 } |
