Removing initial work dir requirement when not needed

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

diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index dec324463d60e5661792a8ad59989b99597c198a..7ae08377f143563bd425ed4314d4b7af8d5a8d39 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -1,17 +1,10 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Generating recalibration table for BQSR 
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Generate recalibration table for BQSR
 
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
@@ -20,14 +13,23 @@ hints:
   ResourceRequirement:
     ramMin: 5000
     coresMin: 2
+  SoftwareRequirement:
+    packages:
+      GATK:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+        version: [ "4.1.7" ]
 
 inputs:
   bam:
     type: File
+    format: edam:format_2572 # BAM
+    label: Indexed sorted BAM with labeled duplicates
     secondaryFiles:
      - .bai
   reference:
     type: File
+    format: edam:format_1929 # FASTA
+    label: Reference genome
     secondaryFiles:
       - .amb
       - .ann
@@ -36,17 +38,23 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: string
-  knownsites1: 
+  sample:
+    type: string
+    label: Sample Name
+  knownsites:
     type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known polymorphic sites for BQSR
     secondaryFiles:
       - .tbi
   intervallist:
     type: File
+    label: Scatter intervals file
 
 outputs:
   recaltable:
     type: File
+    label: Recalibration table for given interval
     outputBinding:
       glob: "*.table"
 
@@ -59,10 +67,23 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - prefix: "--known-sites"
-    valueFrom: $(inputs.knownsites1)
+    valueFrom: $(inputs.knownsites)
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
     valueFrom: $(inputs.sample)_recal_data.table
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ 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