kkonganti@105: process MULTIQC {
kkonganti@105:     label 'process_low'
kkonganti@105:     tag 'MultiQC'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.12" : null)
kkonganti@105:     conda (params.enable_conda ? 'bioconda::multiqc=1.12 conda-forge::spectra conda-forge::lzstring' : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
kkonganti@105:         'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     path multiqc_files
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     path "*multiqc*"
kkonganti@105:     path "*multiqc_report.html", emit: report
kkonganti@105:     path "*_data"              , emit: data
kkonganti@105:     path "*_plots"             , optional: true, emit: plots
kkonganti@105:     path "versions.yml"        , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     """
kkonganti@105:     cp ${params.projectconf}${params.fs}multiqc${params.fs}${params.pipeline}_mqc.yml cpipes_mqc_config.yml
kkonganti@105:     cp ${params.assetsdir}${params.fs}FDa-Logo-Blue---medium-01.png FDa-Logo-Blue---medium-01.png
kkonganti@105:     sed -i -e 's/Workflow_Name_Placeholder/${params.pipeline}/g; s/Workflow_Version_Placeholder/${params.workflow_version}/g' cpipes_mqc_config.yml
kkonganti@105:     sed -i -e 's/CPIPES_Version_Placeholder/${workflow.manifest.version}/g; s%Workflow_Output_Placeholder%${params.output}%g' cpipes_mqc_config.yml
kkonganti@105:     sed -i -e 's%Workflow_Input_Placeholder%${params.input}%g' cpipes_mqc_config.yml
kkonganti@105: 
kkonganti@105:     multiqc -c cpipes_mqc_config.yml -f $args .
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
kkonganti@105:     END_VERSIONS
kkonganti@105: 
kkonganti@105:     sedver=""
kkonganti@105: 
kkonganti@105:     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@105:         sedver=\$( sed --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@105:     else
kkonganti@105:         sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
kkonganti@105:     fi
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS >> versions.yml
kkonganti@105:         sed: \$sedver
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }