kkonganti@0: process NOWAYOUT_RESULTS {
kkonganti@0:     tag "nowayout aggregate"
kkonganti@0:     label "process_pico"
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@0:     conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
kkonganti@0:         'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         path pass_and_fail_rel_abn_files
kkonganti@0:         path lineage_csv
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         path '*.tblsum.txt', emit: mqc_txt, optional: true
kkonganti@0:         path '*_mqc.json'  , emit: mqc_json, optional: true
kkonganti@0:         path '*_mqc.yml'   , emit: mqc_yml, optional: true
kkonganti@0:         path '*.tsv'       , emit: tsv, optional: true
kkonganti@0:         path 'versions.yml', emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:         task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:         def args = task.ext.args ?: ''
kkonganti@0:         """
kkonganti@0:         gen_salmon_tph_and_krona_tsv.py \\
kkonganti@0:             $args \\
kkonganti@0:             -sal "." \\
kkonganti@0:             -smres "." \\
kkonganti@0:             -lin $lineage_csv
kkonganti@0: 
kkonganti@0:         create_mqc_data_table.py \\
kkonganti@0:             "nowayout" "The results shown here are <code>salmon quant</code> TPM values scaled down by a factor of ${params.gsalkronapy_sf}."
kkonganti@0: 
kkonganti@0:         create_mqc_data_table.py \\
kkonganti@0:             "nowayout_indiv_reads_mapped" "The results shown here are the number of reads mapped (post threshold filters) per taxon to the <code>nowayout</code>'s custom <code>${params.db_mode}</code> database for each sample."
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             python: \$( python --version | sed 's/Python //g' )
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: }