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.
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 .
module load nextflow
nextflow run lmsbioinformatics/nf_qc -r v0.1.7 --run_dir ~/mnt/network/isilon_miseq/Runs/240719_M01823_0626_000000000-DMHVJ --outdir 240719_M01823_0626_000000000-DMHVJThe 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 v0.1.7 --run_dir ~/mnt/network/isilon_nextseq/Runs/240730_VH00504_220_2223JLLNX --outdir 240730_VH00504_220_2223JLLNX'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*For a clean slate, cached versions of the pipeline can be deleted if necessary:
module load nextflow
nextflow drop lmsbioinformatics/nf_qc