Bugfix .bai secondary file for ApplyBSQR behavior

[arvados-tutorial.git] / WGS-processing / cwl / helper / gatk-applyBSQR-with-interval.cwl

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index d8f6afd07ecc684d30a4739f9f5cabc39a56eb47..f6d625a09c117a97f43d431cbbe6a02f8de3c94b 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -5,9 +5,6 @@ label: Apply base quality score recalibration
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0

-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)

 
 hints:
   arv:RuntimeConstraints:
 
 hints:
   arv:RuntimeConstraints:


@@ -57,7 +54,7 @@ outputs:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:

-      - .bai
+      - ^.bai

     outputBinding:
       glob: "*nodups_BQSR.bam"
 
     outputBinding:
       glob: "*nodups_BQSR.bam"
 


@@ -70,7 +67,7 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"

-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)

   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"
   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"