Skip to content

Instantly share code, notes, and snippets.

@gkarthik

gkarthik/create_samples.sh

Last active December 18, 2019 08:20
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save gkarthik/61d22bfcfb5c4b69bd6f6edd71ccc39c to your computer and use it in GitHub Desktop.
Save gkarthik/61d22bfcfb5c4b69bd6f6edd71ccc39c to your computer and use it in GitHub Desktop.
Download ZIP
Create samples.tsv
Raw
create_samples.sh
# Naming scheme -> <samplename>_R1.fastq.gz and <samplename>_R2.fastq.gz
echo -e "forward\treverse\tsample\tsample_library" > samples.tsv
find /path/to/folder -name "*.fastq.gz" | sort | xargs -n 2 bash -c 'name=$(basename $0 | cut -f 1 -d _);echo -e "$0\t$1\t${name}\t${name}_L1"' >> samples.tsv
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment