Point transcriptome to ./

2fb61286 · Gervaise Henry · 01a09551 · 2fb61286
Commit 2fb61286 authored 6 years ago by Gervaise Henry
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -76,11 +76,11 @@ process count {
  """
  if (forceCells == 0){
    """
-    cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
    """
  } else {
    """
-    cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
    """
  }
 }