demux.nf

#!/user/bin/nextflow

nextflow.enable.dsl=2

params.samplesheet = "/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/data/nextseq/210408_VH00511_2_AAAFFWNHV/SampleSheet.csv"
params.basecalls = "/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/data/nextseq/210408_VH00511_2_AAAFFWNHV/Data/Intensities/BaseCalls/"
params.runfolder = "/mnt/scgc/scgc_nfs/lab/ggavelis/sandbox/data/nextseq/210408_VH00511_2_AAAFFWNHV/"

params.outdir = "demux_results"

process docker_test {
    tag "demultiplexing reads and writing fastq files"
    module 'singularity/3.8.0'
    publishDir params.outdir
    cpus 24

    input:
    path(samplesheet)

    output:
    tuple path(demultiplexed), path(stats), path(reports), path(interop), emit: demux

    """
    bcl2fastq.py --sample-sheet "${samplesheet}" \
    --input-dir "${params.basecalls}" \
    --runfolder-dir "${params.runfolder}"
    --stats-dir "stats" \
    --reports-dir "reports" \
    --output-dir "demultiplexed" \
    --interop-dir "interop" \
    --loading-threads 12 \
    --processing-threads "${task.cpus}" \
    --writing-threads 12 \
    --barcode-mismatches 0 \
    --no-lane-splitting \
    --no-wait
    """
}


workflow {
    samplesheet_ch = Channel.fromPath( params.samplesheet )
    docker_test(samplesheet_ch)
}