Skip to content

Instantly share code, notes, and snippets.

@fwip

fwip/setup.sh

Created March 17, 2015 00:09
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 fwip/d24cf026d179b39c03fa to your computer and use it in GitHub Desktop.
Save fwip/d24cf026d179b39c03fa to your computer and use it in GitHub Desktop.
Download ZIP
Raw
setup.sh
read -d '' unaligned_command << _U_
bcl2fastq \\\\
--input-dir "${illumina_dir}/Data/Intensities/BaseCalls" \\\\
--use-bases-mask "$mask" \\\\
--output-dir "$fastq_dir" \\\\
--with-failed-reads \\\\
--barcode-mismatches "$mismatches" \\\\
--loading-threads \\\$(( NSLOTS / 4 + 1 )) \\\\
--writing-threads \\\$(( NSLOTS / 4 + 1 )) \\\\
--demultiplexing-threads \\\$(( NSLOTS / 2 + 1 )) \\\\
--processing-threads \\\$(( NSLOTS / 3 + 1 ))
_U_
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment