nf_qc

MRC LMS Nextflow Illumina QC pipeline

nf_qc automates running FastQC and sourmash (in place of FastQ Screen), pulling together the results in a MultiQC report. Where they're available, the pipeline also automatically scrapes the XML files produced by the Illumina machine to fill in run information and will parse the Undetermined_*.fastq.gz files to report the frequency of barcode combinations not included in the sample sheet.

Running

nextflow will automatically pull the pipeline if the it's referenced using its full GitHub name (lmsbioinformatics/nf_qc), though it's good practice to also specify the revision of the pipeline in any case (-r). The pipeline then just requires a --rundir and an --outdir to be specified .

Interactive

module load nextflow
nextflow run lmsbioinformatics/nf_qc -r v0.1.9 --run_dir ~/mnt/network/isilon_miseq/Runs/240719_M01823_0626_000000000-DMHVJ --outdir 240719_M01823_0626_000000000-DMHVJ

As a SLURM Job

The above command can be passed to sbatch using --wrap:

sbatch --job-name nf_qc --partition ctrl --qos qos_ctrl --ntasks 1 --cpus-per-task 1 --mem 512M --time 06:00:00 --parsable --wrap 'module load nextflow; nextflow run lmsbioinformatics/nf_qc -r v0.1.9 --run_dir ~/mnt/network/isilon_nextseq/Runs/240730_VH00504_220_2223JLLNX --outdir 240730_VH00504_220_2223JLLNX'

Tidy Up

A pipeline run will create a work directory and one or more .nextflow.log files that should be deleted after the pipeline has completed:

rm -r work .nextflow.log*

Purging Old Pipeline Versions

For a clean slate, cached versions of the pipeline can be deleted if necessary:

module load nextflow
nextflow drop lmsbioinformatics/nf_qc