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 38e185d5b67e26f299bb39a4b1419cd5893fd9e8..a5d1993652859aacc0430f982f2b50851336d8ac 100644 (file)
--- 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
 cwlVersion: v1.1
 class: Workflow

-label: Variant calling workflow for given interval 
+label: Variant calling workflow for given interval

 
 requirements:
   - class: SubworkflowFeatureRequirement
 
 requirements:
   - class: SubworkflowFeatureRequirement


@@ -24,7 +24,7 @@ inputs:
       - .sa
       - .fai
       - ^.dict
       - .sa
       - .fai
       - ^.dict

-  sample: 
+  sample:

     type: string
     label: Sample Name
   knownsites:
     type: string
     label: Sample Name
   knownsites:


@@ -35,7 +35,7 @@ inputs:
       - .tbi
   intervallist:
     type: File
       - .tbi
   intervallist:
     type: File

-    label: Scatter intervals file 
+    label: Scatter intervals file

 
 outputs:
   gvcf:
 
 outputs:
   gvcf:


@@ -56,7 +56,7 @@ steps:
     out: [recaltable]
   applyBQSR:
     run: gatk-applyBSQR-with-interval.cwl
     out: [recaltable]
   applyBQSR:
     run: gatk-applyBSQR-with-interval.cwl

-    in: 
+    in:

       reference: reference
       bam: bam
       sample: sample
       reference: reference
       bam: bam
       sample: sample


@@ -73,7 +73,7 @@ steps:
     out: [gvcf]
   selectvariants:
     run: gatk-selectvariants.cwl
     out: [gvcf]
   selectvariants:
     run: gatk-selectvariants.cwl

-    in: 
+    in:

       gvcf: haplotypecaller/gvcf
       reference: reference
       sample: sample
       gvcf: haplotypecaller/gvcf
       reference: reference
       sample: sample


@@ -86,6 +86,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
  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 2652233192e1ac1baba00c985046c81b4fba343f..67bf19d0bb4f436eff95e3d86e83bea3f5c06dfe 100644 (file)
--- 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
 hints:
   ResourceRequirement:
     ramMin: 10000

-    coresMin: 4    
+    coresMin: 4

 
 inputs:
   reportfunc:
 
 inputs:
   reportfunc:


@@ -51,6 +51,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
  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 e2aaa887eb27a4efe8239dcd52434673e39b7365..035b4c3135695d3c1607e5d39b4e1f41fb8c6bc6 100644 (file)
--- a/WGS-processing/cwl/helper/getfastq.cwl
+++ b/WGS-processing/cwl/helper/getfastq.cwl
@@ -1,6 +1,6 @@
 class: ExpressionTool
 cwlVersion: v1.1
 class: ExpressionTool
 cwlVersion: v1.1

-label: Find matching FASTQ pairs 
+label: Find matching FASTQ pairs

 requirements:
   InlineJavascriptRequirement: {}
 
 requirements:
   InlineJavascriptRequirement: {}
 


@@ -8,7 +8,7 @@ inputs:
   fastqdir:
     type: Directory
     label: Input directory of FASTQs
   fastqdir:
     type: Directory
     label: Input directory of FASTQs

-    loadListing: 'shallow_listing' 
+    loadListing: 'shallow_listing'

 
 outputs:
   fastq1: 
 
 outputs:
   fastq1: 


@@ -74,6 +74,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
  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