39-use.base.mask

workflow/main.nf

@@ -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}/ \\;