Commit a900c229 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Move ignore dual index before mask and remove i2 from mask

parent ea67847f
Pipeline #7321 failed with stages
in 3 minutes and 8 seconds
......@@ -130,7 +130,7 @@ process mkfastq {
ulimit -u 16384
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --use-bases-mask=Y28n*,I8n*,n*,Y* --ignore-dual-index
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index --use-bases-mask=Y28n*,I8n*,Y*
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
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