kkonganti@1: process BCS_RESULTS {
kkonganti@1:     tag "bettercallsal aggregate"
kkonganti@1:     label "process_pico"
kkonganti@1: 
kkonganti@1:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@1:     conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null)
kkonganti@1:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@1:         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
kkonganti@1:         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
kkonganti@1: 
kkonganti@1:     input:
kkonganti@1:         path salmon_res_dirs
kkonganti@1: 
kkonganti@1:     output:
kkonganti@1:         path 'bettercallsal*.tblsum.txt', emit: mqc_txt, optional: true
kkonganti@1:         path 'bettercallsal*_mqc.json'  , emit: mqc_json, optional: true
kkonganti@1:         path 'bettercallsal*_mqc.yml'   , emit: mqc_yml, optional: true
kkonganti@1:         path 'versions.yml'             , emit: versions
kkonganti@1: 
kkonganti@1:     when:
kkonganti@1:         task.ext.when == null || task.ext.when
kkonganti@1: 
kkonganti@1:     script:
kkonganti@1:         def args = task.ext.args ?: ''
kkonganti@1:         args += (params.tuspy_ps ? " -pickle ${params.tuspy_ps}" : '')
kkonganti@1:         args += (params.gsrpy_snp_clus_metadata ? " -snp ${params.gsrpy_snp_clus_metadata}" : '')
kkonganti@1:         """
kkonganti@1:         gen_salmon_res_table.py \\
kkonganti@1:             $args \\
kkonganti@1:             -sal "."
kkonganti@1: 
kkonganti@1:         create_mqc_data_table.py \\
kkonganti@1:             "bettercallsal" "The following table is an aggregation of serotype calls from all samples which also includes read counts from <code>salmon quant</code> results."
kkonganti@1: 
kkonganti@1:         create_mqc_data_table.py \\
kkonganti@1:             "bettercallsal_salyn" "The following table summarizes serotype presence or absence for all samples."
kkonganti@1: 
kkonganti@1:         cat <<-END_VERSIONS > versions.yml
kkonganti@1:         "${task.process}":
kkonganti@1:             python: \$( python --version | sed 's/Python //g' )
kkonganti@1:         END_VERSIONS
kkonganti@1:         """
kkonganti@1: }