Removing white spaces 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/gvcf-to-vcf.cwl b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
index 305227e9c7e7463f0a58b43be6d2d119b0af835e..4df5fd8b246379dbb55e39e8e862db9cb6b63f65 100644 (file)
--- a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
+++ b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Convert GVCF to VCF 
+label: Convert GVCF to VCF
 
 requirements:
   - class: DockerRequirement
@@ -39,7 +39,7 @@ outputs:
 
 arguments:
   - bcftools
-  - view 
+  - view
   - prefix: "--min-ac"
     valueFrom: "1"
   - $(inputs.gvcf.path)
@@ -62,6 +62,6 @@ $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/mark-duplicates.cwl b/WGS-processing/cwl/helper/mark-duplicates.cwl
index 42efa7ee87b54e73e3de5b7f639508394a0d668f..1a39c1280c830d77867ef9b76f73365be3874f28 100644 (file)
--- a/WGS-processing/cwl/helper/mark-duplicates.cwl
+++ b/WGS-processing/cwl/helper/mark-duplicates.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Mark duplicates using GATK (Picard) 
+label: Mark duplicates using GATK (Picard)
 
 requirements:
   DockerRequirement:
@@ -9,7 +9,7 @@ requirements:
 hints:
   ResourceRequirement:
     ramMin: 20000
-    coresMin: 4    
+    coresMin: 4
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
   SoftwareRequirement:
@@ -22,7 +22,7 @@ inputs:
   bam:
     type: File
     format: edam:format_2572 # BAM
-    label: Sorted BAM 
+    label: Sorted BAM
 
 outputs:
   dupbam:
@@ -41,7 +41,7 @@ baseCommand: /gatk/gatk
 
 arguments:
   - "--java-options"
-  - "-Xmx8G" 
+  - "-Xmx8G"
   - MarkDuplicates
   - prefix: "-I"
     valueFrom: $(inputs.bam.path)
@@ -59,6 +59,6 @@ $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

diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl
index a4c9b2f7ffcda5aabb0c80e4acc145f54c5e3bc1..296e199d3408d9cef89962a63a35e661b86774a0 100644 (file)
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -3,7 +3,7 @@ class: Workflow
 label: Report generation workflow
 
 inputs:
-  gvcf: 
+  gvcf:
     type: File
     format: edam:format_3016 # GVCF
     label: Gathered GVCF
@@ -21,7 +21,7 @@ inputs:
     type: File
     format: edam:format_2331# HTML
     label: Header for HTML report
-  tailhtml:   
+  tailhtml:
     type: File
     format: edam:format_2331 # HTML
     label: Footer for HTML report

diff --git a/WGS-processing/cwl/helper/samtools-index.cwl b/WGS-processing/cwl/helper/samtools-index.cwl
index 76b7402d2c34320ab0db4e525c157ca4b69b16ee..ca6afc726e246866fad71d17ac7bf93bc57c02c1 100644 (file)
--- a/WGS-processing/cwl/helper/samtools-index.cwl
+++ b/WGS-processing/cwl/helper/samtools-index.cwl
@@ -19,7 +19,7 @@ hints:
         version: [ "1.10" ]
 
 inputs:
-  bam: 
+  bam:
     type: File
     format: edam:format_2572 # BAM
     label: Sorted BAM with labeled duplicates
@@ -32,7 +32,7 @@ outputs:
     outputBinding:
       glob: "*bam"
     secondaryFiles:
-      - .bai 
+      - .bai
 
 baseCommand: samtools
 
@@ -49,6 +49,6 @@ $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

diff --git a/WGS-processing/cwl/helper/samtools-sort.cwl b/WGS-processing/cwl/helper/samtools-sort.cwl
index 672dead7a4995f10286bcd344a67d761a39820bd..fa9c0e95c9c28b242c9a9ce01394209031f0a263 100644 (file)
--- a/WGS-processing/cwl/helper/samtools-sort.cwl
+++ b/WGS-processing/cwl/helper/samtools-sort.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Sort BAM 
+label: Sort BAM
 
 requirements:
   DockerRequirement:
@@ -12,7 +12,7 @@ requirements:
 
 hints:
   arv:RuntimeConstraints:
-    keep_cache: 9216 
+    keep_cache: 9216
     outputDirType: keep_output_dir
   SoftwareRequirement:
     packages:
@@ -21,7 +21,7 @@ hints:
         version: [ "1.10" ]
 
 inputs:
-  bam: 
+  bam:
     type: File
     format: edam:format_2572 # BAM
     label: Alignments in BAM format
@@ -33,7 +33,7 @@ outputs:
   sortedbam:
     type: File
     format: edam:format_2572 # BAM
-    label: Sorted BAM 
+    label: Sorted BAM
     outputBinding:
       glob: "*sorted.bam"
 
@@ -58,6 +58,6 @@ $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

diff --git a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
index 2cf48b5f3943b319885af8d207ee43fc02147f0f..75c605b822bf07b8fca8e3e66edc4e152153c014 100644 (file)
--- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: Workflow
-label: Scattered variant calling workflow  
+label: Scattered variant calling workflow
 
 requirements:
   - class: SubworkflowFeatureRequirement
@@ -25,7 +25,7 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
   knownsites:
@@ -34,7 +34,7 @@ inputs:
     label: VCF of known polymorphic sites for BQSR
     secondaryFiles:
       - .tbi
-  scattercount: 
+  scattercount:
     type: string
     label: Desired split for variant calling
 
@@ -42,8 +42,8 @@ outputs:
   gatheredgvcf:
     type: File
     format: edam:format_3016 # GVCF
-    label: Gathered GVCF 
-    secondaryFiles: 
+    label: Gathered GVCF
+    secondaryFiles:
       - .tbi
     outputSource: gather-GVCFs/gatheredgvcf
     
@@ -56,7 +56,7 @@ steps:
       scattercount: scattercount
     out: [intervalfiles]
       
-  recal-haplotypecaller: 
+  recal-haplotypecaller:
     run: gatk-wf-with-interval.cwl
     scatter: intervallist
     in:
@@ -73,7 +73,7 @@ steps:
       gvcfarray: recal-haplotypecaller/gvcf
       sample: sample
       reference: reference
-    out: [gatheredgvcf] 
+    out: [gatheredgvcf]
 
 s:codeRepository: https://github.com/arvados/arvados-tutorial
 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
@@ -82,6 +82,6 @@ $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