Removing white spaces and commenting schemas

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/WGS-processing/cwl/helper/annotate-vcf.cwl b/WGS-processing/cwl/helper/annotate-vcf.cwl
index 41ec58cd35fab6638dd47f2bf078e8d3a032c55a..bb4989e28b48aae7b6e346cbb3dc45e91d08110a 100644 (file)
--- a/WGS-processing/cwl/helper/annotate-vcf.cwl
+++ b/WGS-processing/cwl/helper/annotate-vcf.cwl
@@ -32,6 +32,7 @@ inputs:
 
 outputs:
   reporttxt: stdout
+  label: Annotated text from VCF
 
 arguments:
   - bcftools
@@ -56,6 +57,6 @@ $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/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index 56efe6545d928b4fafdb6b79bce6f8a821761e44..ee8ae4fdce5682340403ba4070a10fc52e1cb1f6 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -6,11 +6,11 @@ requirements:
   - class: SubworkflowFeatureRequirement
 
 inputs:
-  fastq1: 
+  fastq1:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R1)
-  fastq2: 
+  fastq2:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R2)
@@ -91,7 +91,7 @@ steps:
       sample: sample
     out: [bam]
   samtools-sort:
-    run: samtools-sort.cwl 
+    run: samtools-sort.cwl
     in:
       bam: bwamem-samtools-view/bam
       sample: sample
@@ -124,7 +124,7 @@ steps:
       reportfunc: reportfunc
       headhtml: headhtml
       tailhtml: tailhtml
-    out: [report] 
+    out: [report]
 
 s:codeRepository: https://github.com/arvados/arvados-tutorial
 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html

diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
index 0ad81840545acc43bcade1875b554fa0a4086859..32eb5ce0ab53cfbc4b421905ba59bff2b52df716 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
+++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
@@ -8,11 +8,11 @@ requirements:
   ShellCommandRequirement: {}
   ResourceRequirement:
     ramMin: 50000
-    coresMin: 16 
+    coresMin: 16
 
 hints:
   arv:RuntimeConstraints:
-    keep_cache: 1024 
+    keep_cache: 1024
     outputDirType: keep_output_dir
   SoftwareRequirement:
     packages:
@@ -36,15 +36,15 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  fastq1: 
+  fastq1:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R1)
-  fastq2: 
+  fastq2:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R2)
-  sample: 
+  sample:
     type: string
     label: Sample Name
 
@@ -66,7 +66,7 @@ arguments:
   - $(runtime.cores)
   - $(inputs.reference)
   - -R
-  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
+  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
   - -c
   - '250'
   - $(inputs.fastq1)
@@ -91,6 +91,6 @@ $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/fastqc.cwl b/WGS-processing/cwl/helper/fastqc.cwl
index fffcdadffe75c35f8b053becbc73a6e7d6a2d695..30193a12a3a27225ee56ff28dc071e5184fc57d6 100644 (file)
--- a/WGS-processing/cwl/helper/fastqc.cwl
+++ b/WGS-processing/cwl/helper/fastqc.cwl
@@ -14,11 +14,11 @@ hints:
         version: [ "0.11.9" ]
 
 inputs:
-  fastq1: 
+  fastq1:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R1)
-  fastq2: 
+  fastq2:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R2)
@@ -36,7 +36,7 @@ outputs:
     outputBinding:
       glob: "*fastqc.zip"
 
-baseCommand: fastqc 
+baseCommand: fastqc
 
 arguments:
   - $(inputs.fastq1.path)

diff --git a/WGS-processing/cwl/helper/gather-array-vcf.cwl b/WGS-processing/cwl/helper/gather-array-vcf.cwl
deleted file mode 100644 (file)
index 9daf557..0000000
--- a/WGS-processing/cwl/helper/gather-array-vcf.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Gather GVCFs
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
-  DockerRequirement:
-    dockerPull: broadinstitute/gatk:4.1.7.0
-  ShellCommandRequirement: {}
-  InlineJavascriptRequirement: {}
-
-hints:
-  ResourceRequirement:
-    ramMin: 20000
-    coresMin: 4    
-  arv:RuntimeConstraints:
-    outputDirType: keep_output_dir
-
-inputs:
-  gvcfarray: 
-    type: File[] 
-  sample: string
-  reference:
-    type: File
-    secondaryFiles:
-      - .amb
-      - .ann
-      - .bwt
-      - .pac
-      - .sa
-      - .fai
-      - ^.dict
-outputs:
-  gatheredgvcf:
-    type: File
-    secondaryFiles:
-      - .tbi
-    outputBinding:
-      glob: "*.g.vcf.gz"
-
-baseCommand: /gatk/gatk
-
-arguments:
-  - "--java-options"
-  - "-Xmx8G" 
-  - MergeVcfs
-  - shellQuote: false
-    valueFrom: | 
-     ${function compare(a, b) {
-      var baseA = a.basename;
-      var baseB = b.basename;
-
-      var comparison = 0;
-      if (baseA > baseB) {
-      comparison = 1;
-      } else if (baseA < baseB) {
-      comparison = -1;
-      }
-      return comparison;
-      }
-
-      var sortedarray = [];
-      sortedarray = inputs.gvcfarray.sort(compare)
- 
-      var samples = [];
-      for (var i = 0; i < sortedarray.length; i++) {
-        var name = sortedarray[i];
-        if (name.nameext ==='.gz' ) {
-          samples.push(name.path);
-        }
-      }
-     
-      var sampleinput = "";
-
-      for (var i = 0; i < samples.length; i++) {
-       var s1 = samples[i];
-       sampleinput = sampleinput + "-I " + s1 + " "
-      }
-    
-      return sampleinput;
-      }
-  - prefix: "-O"
-    valueFrom: $(inputs.sample).g.vcf.gz

diff --git a/WGS-processing/cwl/helper/gather-vcf.cwl b/WGS-processing/cwl/helper/gather-vcf.cwl
index 15b6551f03d58fed449693976be9e2ba6cdbe654..b59fc351aac0919207ed59f29779ba339dd08c19 100644 (file)
--- a/WGS-processing/cwl/helper/gather-vcf.cwl
+++ b/WGS-processing/cwl/helper/gather-vcf.cwl
@@ -15,16 +15,16 @@ requirements:
 hints:
   ResourceRequirement:
     ramMin: 20000
-    coresMin: 4    
+    coresMin: 4 
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
 
 inputs:
-  gvcfdir: 
+  gvcfdir:
     type: Directory
     label: Input directory of GVCFs
     loadListing: 'shallow_listing'
-  sample: 
+  sample:
     type: string
     label: Sample Name
   reference:
@@ -43,7 +43,7 @@ outputs:
   gatheredgvcf:
     type: File
     format: edam:format_3016 # GVCF
-    label: Gathered GVCF 
+    label: Gathered GVCF
     secondaryFiles:
       - .tbi
     outputBinding:
@@ -53,10 +53,10 @@ baseCommand: /gatk/gatk
 
 arguments:
   - "--java-options"
-  - "-Xmx8G" 
+  - "-Xmx8G"
   - MergeVcfs
   - shellQuote: false
-    valueFrom: | 
+    valueFrom: |
      ${function compare(a, b) {
       var baseA = a.basename;
       var baseB = b.basename;
@@ -68,7 +68,7 @@ arguments:
       comparison = -1;
       }
       return comparison;
-      } 
+      }
 
       var samples = [];
       for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
@@ -99,6 +99,6 @@ $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/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index f9c0fe3ed471cc19b9557c29c5fb0fb28633eae3..d8f6afd07ecc684d30a4739f9f5cabc39a56eb47 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -41,10 +41,10 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
-  recaltable: 
+  recaltable:
     type: File
     label: Recalibration table
   intervallist:
@@ -56,7 +56,7 @@ outputs:
     type: File
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
-    secondaryFiles: 
+    secondaryFiles:
       - .bai
     outputBinding:
       glob: "*nodups_BQSR.bam"
@@ -87,6 +87,6 @@ $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/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index 6df9de12675d1a00af561adb2d874376c9cf4801..80859e64a6eb752e0b67498cc98185adf9421e55 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Generate recalibration table for BQSR 
+label: Generate recalibration table for BQSR
 
 requirements:
   DockerRequirement:
@@ -44,7 +44,7 @@ inputs:
   sample:
     type: string
     label: Sample Name
-  knownsites: 
+  knownsites:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
@@ -87,6 +87,6 @@ $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/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
index 22ce3f6b8a3521d6bca2308b91dfb8b3949f5835..53d7ee209b02d34e59ac96c1cbf34a417dfe28e2 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -9,10 +9,10 @@ requirements:
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
-    keep_cache: 1024 
+    keep_cache: 1024
   ResourceRequirement:
     ramMin: 3500
-    coresMin: 2   
+    coresMin: 2
   SoftwareRequirement:
     packages:
       GATK:
@@ -41,7 +41,7 @@ inputs:
   intervallist:
     type: File
     label: Scatter intervals file
-  sample: 
+  sample:
     type: string
     label: Sample Name
 
@@ -87,6 +87,6 @@ $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/gatk-selectvariants.cwl b/WGS-processing/cwl/helper/gatk-selectvariants.cwl
index 8e7031abe7581905650ac2cd220689357856aaf5..bb5643b50b077ec25467ee8c49f7dd0dfc4343c8 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-selectvariants.cwl
+++ b/WGS-processing/cwl/helper/gatk-selectvariants.cwl
@@ -38,7 +38,7 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
 
@@ -46,7 +46,7 @@ outputs:
   filteredgvcf:
     type: File
     format: edam:format_3016 # GVCF
-    label: Given interval filtered GVCF 
+    label: Given interval filtered GVCF
     outputBinding:
       glob: "*g.vcf.gz"
 
@@ -55,7 +55,7 @@ baseCommand: /gatk/gatk
 arguments:
   - "--java-options"
   - "-Xmx4G"
-  - SelectVariants 
+  - SelectVariants
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "--remove-unused-alternates"
@@ -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

diff --git a/WGS-processing/cwl/helper/gatk-splitintervals.cwl b/WGS-processing/cwl/helper/gatk-splitintervals.cwl
index 9e2644797a107dbc70d942ba25698e8f3072e6ce..98758d1e9e5474c4cb8e2cd7dd6aed3c9af12ee3 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-splitintervals.cwl
+++ b/WGS-processing/cwl/helper/gatk-splitintervals.cwl
@@ -32,10 +32,10 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
-  scattercount: 
+  scattercount:
     type: string
     label: Desired split for variant calling
 
@@ -70,6 +70,6 @@ $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 b53f385d85d690fbe4b7a5d241254f0add9618f4..a4c9b2f7ffcda5aabb0c80e4acc145f54c5e3bc1 100644 (file)
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -63,6 +63,6 @@ $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