From 94165ff5dab6ba9026d1876df4352c2ddb3a089f Mon Sep 17 00:00:00 2001
From: sridhar0605 <sridhar0605@gmail.com>
Date: Thu, 25 Jan 2024 15:02:08 -0600
Subject: [PATCH] indexBam typos

---
 definitions/subworkflows/cram_to_bam_and_index.wdl | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/definitions/subworkflows/cram_to_bam_and_index.wdl b/definitions/subworkflows/cram_to_bam_and_index.wdl
index f35055d..e8f36b3 100644
--- 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
     }
 }
\ No newline at end of file