X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/611c455f8a94ab5dbd5c94415802b5c7fd009ffc..c604c42bb92a6301b13a250582eabed509adaae1:/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 d8f6afd..f6d625a 100644
--- 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
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
@@ -57,7 +54,7 @@ outputs:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:
-      - .bai
+      - ^.bai
     outputBinding:
       glob: "*nodups_BQSR.bam"
 
@@ -70,7 +67,7 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"