Adding labels and metadata

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index 33a1feb9cabbbfc04afee918e6cdadae92a1db89..f9c0fe3ed471cc19b9557c29c5fb0fb28633eae3 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -2,10 +2,6 @@ cwlVersion: v1.1
 class: CommandLineTool
 label: Apply base quality score recalibration 
 
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
@@ -20,14 +16,23 @@ 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
@@ -36,15 +41,21 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: string
+  sample: 
+    type: string
+    label: Sample Name
   recaltable: 
     type: File
+    label: Recalibration table
   intervallist:
     type: File
+    label: Scatter intervals file
 
 outputs:
   recalbam:
     type: File
+    format: edam:format_2572 # BAM
+    label: Recalibrated BAM for given interval
     secondaryFiles: 
       - .bai
     outputBinding:
@@ -66,3 +77,16 @@ arguments:
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
     valueFrom: $(inputs.sample)nodups_BQSR.bam
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$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

diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index 2ad23b7f8dc22ed0e6da2de068af5d1d08c0e612..7e5bf4df4bc863807a4136547ab794af374cb69e 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -57,7 +57,7 @@ inputs:
 outputs:
   recaltable:
     type: File
-    label: Recalibration table
+    label: Recalibration table for given interval
     outputBinding:
       glob: "*.table"