diff --git a/workflow/main.nf b/workflow/main.nf index 294f3fa58cf06527833779081d0523650008710e..7fef409383c9ca5bca8dabe1b38949aeb21d79a1 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -71,15 +71,14 @@ process count { file("**/outs/**") into outPaths script: - """ - module load cellranger/2.1.1 - """ if (forceCells == 0){ """ + module load cellranger/2.1.1 cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells """ } else { """ + module load cellranger/2.1.1 cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells """ }