Merge pull request #62 from tmooney/reconcile_no_validatesamfile

Port some fixes from no_validatesamfile to master.
genome · Aug 16, 2021 · 3eec411 · 3eec411
2 parents d47251d + c7dc14d
commit 3eec411
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/SingleSampleQc.wdl b/SingleSampleQc.wdl
@@ -24,7 +24,7 @@ version 1.0
 ## - [VerifyBamID2](https://github.com/Griffan/VerifyBamID)
 
 # Git URL import
-import "https://raw.githubusercontent.com/genome/qc-analysis-pipeline/master/tasks/Qc.wdl" as QC
+import "tasks/Qc.wdl" as QC
 
 # WORKFLOW DEFINITION
 workflow SingleSampleQc {
@@ -187,6 +187,7 @@ workflow SingleSampleQc {
     File? hs_metrics = CollectHsMetrics.metrics
 
     File input_bam_md5 = CalculateChecksum.md5
+    String input_bam_md5_hash = CalculateChecksum.md5_hash
     File input_bam_index = BuildBamIndex.bam_index
   }
 }
diff --git a/tasks/Qc.wdl b/tasks/Qc.wdl
@@ -408,8 +408,10 @@ task CalculateChecksum {
 
   Int disk_size = ceil(size(input_bam, "GiB")) + 20
 
+  String output_name = basename(input_bam)
+
   command {
-    md5sum ~{input_bam} > ~{input_bam}.md5
+    md5sum ~{input_bam} > ~{output_name}.md5
   }
   runtime {
     preemptible: preemptible_tries
@@ -418,6 +420,7 @@ task CalculateChecksum {
     docker: "us.gcr.io/gcp-runtimes/ubuntu_16_0_4:latest"
   }
   output {
-    File md5 = "~{input_bam}.md5"
+    File md5 = "~{output_name}.md5"
+    String md5_hash = sub(read_string(md5), " .+$", "")
   }
 }