Bugfix .bai secondary file for ApplyBSQR behavior

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

diff --git a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
index 22ce3f6b8a3521d6bca2308b91dfb8b3949f5835..0b6c1029ddc3f135ec39fbb834587906f336ffe3 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -9,10 +9,10 @@ requirements:
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
-    keep_cache: 1024 
+    keep_cache: 1024
   ResourceRequirement:
     ramMin: 3500
-    coresMin: 2   
+    coresMin: 2
   SoftwareRequirement:
     packages:
       GATK:
@@ -25,7 +25,7 @@ inputs:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:
-      - .bai
+      - ^.bai
   reference:
     type: File
     format: edam:format_1929 # FASTA
@@ -41,7 +41,7 @@ inputs:
   intervallist:
     type: File
     label: Scatter intervals file
-  sample: 
+  sample:
     type: string
     label: Sample Name
 
@@ -68,7 +68,7 @@ arguments:
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
-    valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
+    valueFrom: $(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
   - prefix: "-ERC"
     valueFrom: "GVCF"
   - prefix: "-GQB"
@@ -87,6 +87,6 @@ $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