Removing initial work dir requirement when not needed

[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 f9c0fe3ed471cc19b9557c29c5fb0fb28633eae3..52413a6ea4958dd60c2d433ee1af308decb9b0b8 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
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
@@ -41,10 +38,10 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
-  recaltable: 
+  recaltable:
     type: File
     label: Recalibration table
   intervallist:
@@ -56,7 +53,7 @@ outputs:
     type: File
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
-    secondaryFiles: 
+    secondaryFiles:
       - .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"
@@ -87,6 +84,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl