Merge pull request #52 from ctg-lund/aln

support for alignment
ctg-lund · Nov 2, 2023 · ed5fd45 · ed5fd45
2 parents 1968a70 + 87d0d44
commit ed5fd45
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/modules/spaceranger/main.nf b/modules/spaceranger/main.nf
@@ -43,6 +43,12 @@ process SPACECOUNT {
 	else {
 		image_argument = ""
 	}
+	if ( alignment != "n") {
+		alignment_argument = "--loupe-alignment="+params.outdir+'/'+Sample_Project+'/metadata/'+alignment
+		}
+	else {
+		alignment_argument = ""
+	}
 
 
     """
@@ -58,6 +64,7 @@ process SPACECOUNT {
 			$dark_argument \
 			$cyta_argument \
 			$probe_argument \
+			$alignment_argument \
     """
 	stub:
 	"""