qc_report.nf

process QC_REPORT {
    tag "$meta.id"
    label 'process_low'

    conda (params.enable_conda ? "bioconda::pandas=1.1.5" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/pandas:1.1.5' : 
        'quay.io/biocontainers/pandas:1.1.5' }"
        
    input:
    tuple val(meta), path(txt)
    path reference

    output:
    tuple val(meta), path("output.txt"), emit: qc_stuff

    script:
    def args = task.ext.args ?: '' 
    def prefix = task.ext.prefix ?: "${meta.id}"

    """
    
    python $projectDir/bin/qc_report_stats.py \\
        --sample ${meta.id} \\
        --stats ${meta.id}.stats.txt \\
        --base_content_before_trim qa.${meta.id}.base_content.txt \\
        --base_content_after_trim ${meta.id}.base_content.txt \\
        --qual_scores_before_trim ${meta.id}.for_qual_histogram.txt \\
        --qual_scores_after_trim qa.${meta.id}.for_qual_histogram.txt \\
        --reference ${reference} > output.txt
    
    """
    // results need to be collected and put into the same csv spreadsheet
}
//#REFERENCE_LEN=\$(awk '!/^>/ {len+=length(\$0)} END {print len}' < ${reference})