Adding more labels

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

diff --git a/WGS-processing/cwl/helper/.samtools-sort.cwl.swp b/WGS-processing/cwl/helper/.samtools-sort.cwl.swp
deleted file mode 100644 (file)
index 8279731..0000000
Binary files a/WGS-processing/cwl/helper/.samtools-sort.cwl.swp and /dev/null differ

diff --git a/WGS-processing/cwl/helper/mark-duplicates.cwl b/WGS-processing/cwl/helper/mark-duplicates.cwl
index 6041221bf8718d502ea69c45fe721d39f25dcb53..42efa7ee87b54e73e3de5b7f639508394a0d668f 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
 cwlVersion: v1.1
 class: CommandLineTool

-label: Marking Duplicates using GATK (Picard) 
+label: Mark duplicates using GATK (Picard) 

 
 requirements:
   DockerRequirement:
 
 requirements:
   DockerRequirement:

diff --git a/WGS-processing/cwl/helper/samtools-index.cwl b/WGS-processing/cwl/helper/samtools-index.cwl
index d479fbd5d5a45f857103729c8e9942469b2b46a8..76b7402d2c34320ab0db4e525c157ca4b69b16ee 100644 (file)
--- a/WGS-processing/cwl/helper/samtools-index.cwl
+++ b/WGS-processing/cwl/helper/samtools-index.cwl
@@ -1,10 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
 cwlVersion: v1.1
 class: CommandLineTool

-label: Indexing Bam File
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Index BAM

 
 requirements:
   DockerRequirement:
 
 requirements:
   DockerRequirement:


@@ -16,20 +12,43 @@ requirements:
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir

+  SoftwareRequirement:
+    packages:
+      Samtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+        version: [ "1.10" ]

 
 inputs:
 
 inputs:

-  bam: File
+  bam: 
+    type: File
+    format: edam:format_2572 # BAM
+    label: Sorted BAM with labeled duplicates

 
 outputs:
   indexedbam:
     type: File
 
 outputs:
   indexedbam:
     type: File

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

     outputBinding:
       glob: "*bam"
     secondaryFiles:
     outputBinding:
       glob: "*bam"
     secondaryFiles:

-      - .bai
+      - .bai 

 
 baseCommand: samtools
 
 arguments:
   - index
   - $(inputs.bam.basename)
 
 baseCommand: samtools
 
 arguments:
   - index
   - $(inputs.bam.basename)

+
+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

diff --git a/WGS-processing/cwl/helper/samtools-sort.cwl b/WGS-processing/cwl/helper/samtools-sort.cwl
index 88950e3dff096e85954e44933bcb87f716887cdc..672dead7a4995f10286bcd344a67d761a39820bd 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
 cwlVersion: v1.1
 class: CommandLineTool

-label: Sorting BAM file
+label: Sort BAM 

 
 requirements:
   DockerRequirement:
 
 requirements:
   DockerRequirement: