Commit 1faeefff authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

39-use.base.mask

parent 6e066038
Pipeline #7319 failed with stages
in 5 minutes and 58 seconds
......@@ -127,7 +127,7 @@ process mkfastq {
"""
hostname
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --ignore-dual-index
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --use-bases-mask=Y28n*,I8n*,n*,Y* --ignore-dual-index
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
......
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