From 75c24ab82debc1ed5bea2f02425c12fa31febc3c Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 25 Jun 2020 01:26:02 +0000
Subject: [PATCH 1/1] Adding more labels Arvados-DCO-1.1-Signed-off-by: Sarah
 Wait Zaranek <swz@curii.com> no issue #

---
 .../cwl/helper/.samtools-sort.cwl.swp         | Bin 12288 -> 0 bytes
 WGS-processing/cwl/helper/mark-duplicates.cwl |   2 +-
 WGS-processing/cwl/helper/samtools-index.cwl  |  33 ++++++++++++++----
 WGS-processing/cwl/helper/samtools-sort.cwl   |   2 +-
 4 files changed, 28 insertions(+), 9 deletions(-)
 delete mode 100644 WGS-processing/cwl/helper/.samtools-sort.cwl.swp

diff --git a/WGS-processing/cwl/helper/.samtools-sort.cwl.swp b/WGS-processing/cwl/helper/.samtools-sort.cwl.swp
deleted file mode 100644
index 82797313cf62ffcb01fb2983f75a26dc2d75c951..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/WGS-processing/cwl/helper/mark-duplicates.cwl b/WGS-processing/cwl/helper/mark-duplicates.cwl
index 6041221..42efa7e 100644
--- 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: Marking Duplicates using GATK (Picard) 
+label: Mark duplicates using GATK (Picard) 
 
 requirements:
   DockerRequirement:
diff --git a/WGS-processing/cwl/helper/samtools-index.cwl b/WGS-processing/cwl/helper/samtools-index.cwl
index d479fbd..76b7402 100644
--- 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
-label: Indexing Bam File
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Index BAM
 
 requirements:
   DockerRequirement:
@@ -16,20 +12,43 @@ requirements:
 hints:
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
+  SoftwareRequirement:
+    packages:
+      Samtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+        version: [ "1.10" ]
 
 inputs:
-  bam: File
+  bam: 
+    type: File
+    format: edam:format_2572 # BAM
+    label: Sorted BAM with labeled duplicates
 
 outputs:
   indexedbam:
     type: File
+    format: edam:format_2572 # BAM
+    label: Indexed sorted BAM with labeled duplicates 
     outputBinding:
       glob: "*bam"
     secondaryFiles:
-      - .bai
+      - .bai 
 
 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 88950e3..672dead 100644
--- 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: Sorting BAM file
+label: Sort BAM 
 
 requirements:
   DockerRequirement:
-- 
2.30.2