indexBam typos

wustl-oncology · Jan 25, 2024 · 94165ff · 94165ff
1 parent c5a60f7
commit 94165ff
Showing 1 changed file with 5 additions and 6 deletions.
diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl
@@ -17,18 +17,17 @@ workflow cramTobamAndIndex{
         cram=cram,
         cram_index=cram_index,
         reference=reference,
-        reference_fai=reference_fai,
+        reference_fai=reference_index,
         reference_dict=reference_dict
     }
 
     call i.indexBam {
-        input:
-        bam=cramToBam.bam
+        input: bam=cramToBam.bam
     }
 
     output {
-        File indexed_bam = index_bam.indexed_bam
-        File indexed_bam_bai = index_bam.indexed_bam_bai
-        File indexed_bai = index_bam.indexed_bai
+        File indexed_bam = indexBam.indexed_bam
+        File indexed_bam_bai = indexBam.indexed_bam_bai
+        File indexed_bai = indexBam.indexed_bai
     }
 }