Bugfix .bai secondary file for ApplyBSQR behavior

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

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index 41cfd2e3e195575b642b3476fd9739e275049869..f6d625a09c117a97f43d431cbbe6a02f8de3c94b 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -1,17 +1,10 @@
 cwlVersion: v1.1
 class: CommandLineTool
 cwlVersion: v1.1
 class: CommandLineTool

-label: Applying base quality score recalibration 
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Apply base quality score recalibration 

 
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
 
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0

-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)

 
 hints:
   arv:RuntimeConstraints:
 
 hints:
   arv:RuntimeConstraints:


@@ -20,14 +13,23 @@ hints:
   ResourceRequirement:
     ramMin: 5000
     coresMin: 2
   ResourceRequirement:
     ramMin: 5000
     coresMin: 2

+  SoftwareRequirement:
+    packages:
+      GATK:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+        version: [ "4.1.7" ]

 
 inputs:
   bam:
     type: File
 
 inputs:
   bam:
     type: File

+    format: edam:format_2572 # BAM
+    label: Indexed sorted BAM with labeled duplicates

     secondaryFiles:
       - .bai
   reference:
     type: File
     secondaryFiles:
       - .bai
   reference:
     type: File

+    format: edam:format_1929 # FASTA
+    label: Reference genome

     secondaryFiles:
       - .amb
       - .ann
     secondaryFiles:
       - .amb
       - .ann


@@ -36,17 +38,23 @@ inputs:
       - .sa
       - .fai
       - ^.dict
       - .sa
       - .fai
       - ^.dict

-  sample: string
-  recaltable: 
+  sample:
+    type: string
+    label: Sample Name
+  recaltable:

     type: File
     type: File

+    label: Recalibration table

   intervallist:
     type: File
   intervallist:
     type: File

+    label: Scatter intervals file

 
 outputs:
   recalbam:
     type: File
 
 outputs:
   recalbam:
     type: File

-    secondaryFiles: 
-      - .bai
+    format: edam:format_2572 # BAM
+    label: Recalibrated BAM for given interval
+    secondaryFiles:
+      - ^.bai

     outputBinding:
       glob: "*nodups_BQSR.bam"
 
     outputBinding:
       glob: "*nodups_BQSR.bam"
 


@@ -59,10 +67,23 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"

-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)

   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
     valueFrom: $(inputs.sample)nodups_BQSR.bam
   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"
     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