How zip up a folder of loose FASTQ files

Posted on July 16, 2020

The problem is to find all fastq files, and submit each one, one by one as a job to be gzipped.

ls *.fastq | xargs -I {} gzip {}

Multicore version

You will need to have pigz installed.

ls *.fastq | xargs -I {} pigz {}

This really applies if you are working on a computing cluster (SLURM).

ls *.fastq | xargs -I {} sbatch --wrap="gzip {}"

Multicore version

You will need to have pigz installed.

ls *.fastq | xargs -I {} sbatch --wrap="pigz {}"