preprocess_qc.config

process {
    withName: SAMPLESHEET_CHECK {
        publishDir = [
            path: { "${params.outdir}/0_pipeline_info" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
    }

    withName: FASTQC_RAW {
        publishDir = [
            path: { "${params.outdir}/2_qc_and_umi/2a_fastqc/fastq_raw" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
        ext.args = '--quiet'
    }

    withName: CAT_FASTQ {
      publishDir = [
          path: { "${params.outdir}/1_preprocess/1a_lane_merge" },
          mode: params.publish_dir_fastq,
          saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
      ]
    }

    withName: UMI_EXTRACT {
        publishDir = [
            path: { "${params.outdir}/1_preprocess/1b_umi_extract" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
        ext.args = '--bc-pattern=NNNNNNNNNN'
    }

    withName: CUTADAPT {
        publishDir = [
            path: { "${params.outdir}/1_preprocess/1c_cutadapt" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
        ext.args = '-g GTAGGCTCCAAGTCTTCAGGGTCTGT -G CGGCTGAGGCAGCAGCGGCTGT'
    }

    withName: FASTQC_CUTADAPT {
        publishDir = [
            path: { "${params.outdir}/2_qc_and_umi/2a_fastqc/fastq_cutadapt" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
        ext.args = '--quiet'
    }

    withName: READ_PER_UMI {
        publishDir = [
            path: { "${params.outdir}/2_qc_and_umi/2b_read_per_umi_cutadapt" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
        ext.args = '500' // X-axis range: choose from 'auto' or a positive number; if 'auto', the X-axis scale of the plot will be automatically determined.
    }
}