Merge pull request #96 from Oliver-Lorenz-dev/remove-reference-from-c…

…ram-decode-farm5 remove ref from cram decode (farm5)
malariagen · Nov 12, 2021 · 4cd0e23 · 4cd0e23
2 parents baec7b6 + 557dfa3
commit 4cd0e23
Show file tree

Hide file tree

Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/tasks/farm5/Alignment.wdl b/tasks/farm5/Alignment.wdl
@@ -37,7 +37,6 @@ workflow Alignment {
       input:
         input_file = input_cram,
         output_filename = output_file_basename + ".bam",
-        reference = reference,
         runTimeSettings = runTimeSettings
     }
   }

diff --git a/tasks/farm5/ShortReadAlignmentTasks.wdl b/tasks/farm5/ShortReadAlignmentTasks.wdl
@@ -94,7 +94,6 @@ task CramToBam {
     Int memory = 3000
     String? lsf_group
     String? lsf_queue
-    ReferenceSequence reference
     RunTimeSettings runTimeSettings
   }
 
@@ -103,7 +102,7 @@ task CramToBam {
     set -e
     set -o pipefail
 
-    samtools view -h -T ~{reference.ref_fasta} ~{input_file} |
+    samtools view -h ~{input_file} |
     samtools view -b -o ~{output_filename} -
     samtools index -b ~{output_filename}