From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 2 Jul 2020 16:28:54 +0000 (+0000)
Subject: Removing white space and commenting out schemas
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/d793af44f649b6305f14e4ac4927e22245d17084

Removing white space and commenting out schemas
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index 38e185d..a5d1993 100644
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: Workflow
-label: Variant calling workflow for given interval 
+label: Variant calling workflow for given interval
 
 requirements:
   - class: SubworkflowFeatureRequirement
@@ -24,7 +24,7 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
   knownsites:
@@ -35,7 +35,7 @@ inputs:
       - .tbi
   intervallist:
     type: File
-    label: Scatter intervals file 
+    label: Scatter intervals file
 
 outputs:
   gvcf:
@@ -56,7 +56,7 @@ steps:
     out: [recaltable]
   applyBQSR:
     run: gatk-applyBSQR-with-interval.cwl
-    in: 
+    in:
       reference: reference
       bam: bam
       sample: sample
@@ -73,7 +73,7 @@ steps:
     out: [gvcf]
   selectvariants:
     run: gatk-selectvariants.cwl
-    in: 
+    in:
       gvcf: haplotypecaller/gvcf
       reference: reference
       sample: sample
@@ -86,6 +86,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
diff --git a/WGS-processing/cwl/helper/generate-report.cwl b/WGS-processing/cwl/helper/generate-report.cwl
index 2652233..67bf19d 100644
--- a/WGS-processing/cwl/helper/generate-report.cwl
+++ b/WGS-processing/cwl/helper/generate-report.cwl
@@ -9,7 +9,7 @@ requirements:
 hints:
   ResourceRequirement:
     ramMin: 10000
-    coresMin: 4    
+    coresMin: 4
 
 inputs:
   reportfunc:
@@ -51,6 +51,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
diff --git a/WGS-processing/cwl/helper/getfastq.cwl b/WGS-processing/cwl/helper/getfastq.cwl
index e2aaa88..035b4c3 100644
--- a/WGS-processing/cwl/helper/getfastq.cwl
+++ b/WGS-processing/cwl/helper/getfastq.cwl
@@ -1,6 +1,6 @@
 class: ExpressionTool
 cwlVersion: v1.1
-label: Find matching FASTQ pairs 
+label: Find matching FASTQ pairs
 requirements:
   InlineJavascriptRequirement: {}
 
@@ -8,7 +8,7 @@ inputs:
   fastqdir:
     type: Directory
     label: Input directory of FASTQs
-    loadListing: 'shallow_listing' 
+    loadListing: 'shallow_listing'
 
 outputs:
   fastq1: 
@@ -74,6 +74,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl