millironx/sc2-sequencing
1
0
Fork 0
mirror of https://github.com/MillironX/sc2-sequencing.git synced 2024-12-22 03:08:17 +00:00
Code Issues Releases Packages Activity

Fix hardcoded task number to unzip fastqs

Browse source
This commit is contained in:
Thomas A. Christensen II 2021-03-30 08:52:23 -06:00 committed by GitHub
parent 25625085d3
commit 254751899d
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 1 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
ont/ont-demux
View file

@ -14,7 +14,7 @@ OUTNAME="$RUNNAME"_demux
guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100% guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100%
# Unzip the fastqs # Unzip the fastqs
parallel --gnu -j12 --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz parallel --gnu -j"$NUMCPU" --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz
# Squish them together # Squish them together
cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq