X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/cec9a7f6a83fc2596e042e8adc6179b202f92a6e..c604c42bb92a6301b13a250582eabed509adaae1:/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 88c78e0..0b6c102 100644
--- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -1,10 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Germline variant calling using GATK with output gvcf
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Call variants with GATK HaplotypeCaller
 
 requirements:
   DockerRequirement:
@@ -13,18 +9,27 @@ requirements:
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
-    keep_cache: 1024 
+    keep_cache: 1024
   ResourceRequirement:
     ramMin: 3500
-    coresMin: 2   
+    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: Recalibrated BAM for given interval
     secondaryFiles:
-      - .bai
+      - ^.bai
   reference:
     type: File
+    format: edam:format_1929 # FASTA
+    label: Reference genome
     secondaryFiles:
       - .amb
       - .ann
@@ -35,11 +40,16 @@ inputs:
       - ^.dict
   intervallist:
     type: File
-  sample: string
+    label: Scatter intervals file
+  sample:
+    type: string
+    label: Sample Name
 
 outputs:
   gvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: GVCF for given interval
     secondaryFiles:
       - .tbi
     outputBinding:
@@ -58,7 +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"
@@ -67,3 +77,16 @@ arguments:
     valueFrom: "20"
   - prefix: "-GQB"
     valueFrom: "60"
+
+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