Add back ignor-dual-index

8d3bb432 · Gervaise Henry · 379a4778 · 8d3bb432
Commit 8d3bb432 authored Oct 30, 2020 by Gervaise Henry 🤠
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workflow/main.nf workflow/main.nf +1 -1

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--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -188,7 +188,7 @@ process mkfastq {
    hostname
    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}/ \\;