Fixing labels for knownsites

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

diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index c7bd8021f8ed0ad9d9018201e281c2b04dd3c37e..b3ea17f6eefda46ac0616ae4eeee0d4507768d73 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -1,16 +1,21 @@
 cwlVersion: v1.1
 class: Workflow
+label: Variant calling workflow for given interval
 
 requirements:
-  - class: SubworkflowFeatureRequirement
+  SubworkflowFeatureRequirement: {}
 
 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
@@ -19,32 +24,46 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: string
+  sample:
+    type: string
+    label: Sample Name
   knownsites1:
     type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known SNPS sites for BQSR
+    secondaryFiles:
+      - .idx
+  knownsites2:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known indel sites for BQSR
     secondaryFiles:
       - .tbi
   intervallist:
     type: File
+    label: Scatter intervals file
 
 outputs:
   gvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: Given interval filtered GVCF
     outputSource: selectvariants/filteredgvcf
 
 steps:
   basecalibrator:
-    run: ./helper/gatk-baserecalibrator-with-interval.cwl
+    run: gatk-baserecalibrator-with-interval.cwl
     in:
       bam: bam
       reference: reference
       sample: sample
       knownsites1: knownsites1
+      knownsites2: knownsites2
       intervallist: intervallist
     out: [recaltable]
   applyBQSR:
-    run: ./helper/gatk-applyBSQR-with-interval.cwl
-    in: 
+    run: gatk-applyBSQR-with-interval.cwl
+    in:
       reference: reference
       bam: bam
       sample: sample
@@ -52,7 +71,7 @@ steps:
       recaltable: basecalibrator/recaltable
     out: [recalbam]
   haplotypecaller:
-    run: ./helper/gatk-haplotypecaller-with-interval.cwl
+    run: gatk-haplotypecaller-with-interval.cwl
     in:
       reference: reference
       bam: applyBQSR/recalbam
@@ -60,9 +79,20 @@ steps:
       intervallist: intervallist
     out: [gvcf]
   selectvariants:
-    run: ./helper/gatk-selectvariants.cwl
-    in: 
+    run: gatk-selectvariants.cwl
+    in:
       gvcf: haplotypecaller/gvcf
       reference: reference
       sample: sample
     out: [filteredgvcf]
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl