Incorrect Handling of Contamination Values

[ramsainanduri]

two different args for tumor and normal in the config were parsed with the same arg variable name

    withName: '.*SNV_ANNOTATE:CONTAMINATION' {
        container = "${params.container_dir}/perl-gd.sif"

        publishDir = [
            [ 
                path: "${params.outdir}/${params.subdir}/QC/contamination",
                mode: 'copy',
                overwrite: true,
                pattern: "*.png",
            ],
            [ 
                path: "${params.outdir}/${params.subdir}/QC/contamination",
                mode: 'copy',
                overwrite: true,
                pattern: "*.txt",
            ],
            [ 
                path: "${params.crondir}/contamination",
                mode: 'copy',
                overwrite: true,
                pattern: "*.contaminationpy",
            ],
        ]

        ext.args    = { "--assay ${params.cdm} --detect-level 0.01" }
        ext.args    = { "--assay ${params.cdm} --detect-level 0.01 --normal" }
    }

[ramsainanduri]

Hot fixed in the commit ebae012