Add back ignor-dual-index

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}/ \\;