changing barcode_kit option in guppy_barcoder into a variable

aryeelab · Jul 24, 2023 · 6846659 · 6846659
1 parent ec416bf
commit 6846659
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/demux.wdl b/demux.wdl
@@ -6,11 +6,13 @@ workflow demux {
         File infastq
         File reads
         File pythonscript
+        String barcodekit
     }
 
     call guppybarcoder {
         input:
-            infastq=infastq
+            infastq=infastq,
+            barcodekit=barcodekit
     }
     call makefast5s {
         input:
@@ -37,12 +39,13 @@ workflow demux {
 task guppybarcoder  {
     input {
         File infastq
+        String barcodekit
     }
     command <<<
     mkdir out
     mkdir in
     cp ~{infastq} ./in
-    guppy_barcoder -i ./in -s ./out --barcode_kits SQK-RBK114-24 #--enable_trim_barcodes
+    guppy_barcoder -i ./in -s ./out ~{barcodekit} #--enable_trim_barcodes
     for f in ./out/*; do
         dir_name="${f##*/}"
         cat "$f"/*.fastq > ./out/"$dir_name".fastq