seq-contamination-QC-nf

Nextflow workflow - Fastq screen contamination check and FastQC report

you can run this workflow using the following command

nextflow run AgBC-UoP/seq-contamination-QC-nf -r main --reads {readDir/READ_PATTERN}

ex : nextflow run AgBC-UoP/seq-contamination-QC-nf -r main --reads "*R{1,2}*.fastq"

optioinal commands:

--fastqs_conf - path to fastqc_screen config file

--fastqs_subset - subset read count