Commit 8d3bb432 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add back ignor-dual-index

parent 379a4778
Pipeline #8255 failed with stages
in 4 minutes and 24 seconds
......@@ -188,7 +188,7 @@ process mkfastq {
ulimit -u 16384
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} ${mask}
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index ${mask}
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
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