kkonganti@101: process TABLE_SUMMARY {
kkonganti@101:     tag "$table_sum_on"
kkonganti@101:     label 'process_low'
kkonganti@101: 
kkonganti@101:     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
kkonganti@101:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@101:     conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml conda-forge::coreutils" : null)
kkonganti@101:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@101:         'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
kkonganti@101:         'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
kkonganti@101: 
kkonganti@101:     input:
kkonganti@101:     tuple val(table_sum_on), path(tables)
kkonganti@101: 
kkonganti@101:     output:
kkonganti@101:     tuple val(table_sum_on), path("*.tblsum.txt"), emit: tblsummed
kkonganti@101:     path "*_mqc.yml"                             , emit: mqc_yml
kkonganti@101:     path "versions.yml"                          , emit: versions
kkonganti@101: 
kkonganti@101:     when:
kkonganti@101:     task.ext.when == null || task.ext.when || tables
kkonganti@101: 
kkonganti@101:     script:
kkonganti@101:     def args = task.ext.args ?: ''
kkonganti@101:     def onthese = tables.collect().join('\\n')
kkonganti@101:     """
kkonganti@101:     filenum="1"
kkonganti@101:     header=""
kkonganti@101: 
kkonganti@101:     echo -e "$onthese" | while read -r file; do
kkonganti@101:         
kkonganti@101:         if [ "\${filenum}" == "1" ]; then
kkonganti@101:             header=\$( head -n1 "\${file}" )
kkonganti@101:             echo -e "\${header}" > ${table_sum_on}.tblsum.txt
kkonganti@101:         fi
kkonganti@101: 
kkonganti@101:         tail -n+2 "\${file}" >> ${table_sum_on}.tblsum.txt
kkonganti@101: 
kkonganti@101:         filenum=\$((filenum+1))
kkonganti@101:     done
kkonganti@101: 
kkonganti@101:     create_mqc_data_table.py $table_sum_on ${workflow.manifest.name}
kkonganti@101: 
kkonganti@101:     cat <<-END_VERSIONS > versions.yml
kkonganti@101:     "${task.process}":
kkonganti@101:         bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@101:         python: \$( python --version | sed 's/Python //g' )
kkonganti@101:     END_VERSIONS
kkonganti@101: 
kkonganti@101:     headver=""
kkonganti@101:     tailver=""
kkonganti@101: 
kkonganti@101:     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@101:         headver=\$( head --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@101:         tailver="\$headver"
kkonganti@101:     else
kkonganti@101:         headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@101:         tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@101:     fi
kkonganti@101: 
kkonganti@101:     cat <<-END_VERSIONS >> versions.yml
kkonganti@101:         head: \$headver
kkonganti@101:         tail: \$tailver
kkonganti@101:     END_VERSIONS
kkonganti@101:     """
kkonganti@101: }