From cc79dd8213409bc57dd731687c9f67c9a84808bb Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Wed, 13 Jul 2016 17:32:32 -0400
Subject: [PATCH] 9369: Update tutorial to CWL v1.0

---
 doc/user/cwl/bwa-mem/bwa-mem-input-local.yml |  6 +--
 doc/user/cwl/bwa-mem/bwa-mem-input.yml       |  6 +--
 doc/user/cwl/bwa-mem/bwa-mem-template.yml    |  2 +-
 doc/user/cwl/bwa-mem/bwa-mem.cwl             | 39 ++++++++------------
 4 files changed, 23 insertions(+), 30 deletions(-)

diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input-local.yml b/doc/user/cwl/bwa-mem/bwa-mem-input-local.yml
index 7f8c7bdb72..13aad6d7d3 100755
--- a/doc/user/cwl/bwa-mem/bwa-mem-input-local.yml
+++ b/doc/user/cwl/bwa-mem/bwa-mem-input-local.yml
@@ -2,13 +2,13 @@
 cwl:tool: bwa-mem.cwl
 reference:
   class: File
-  path: 19.fasta.bwt
+  location: 19.fasta.bwt
 read_p1:
   class: File
-  path: HWI-ST1027_129_D0THKACXX.1_1.fastq
+  location: HWI-ST1027_129_D0THKACXX.1_1.fastq
 read_p2:
   class: File
-  path: HWI-ST1027_129_D0THKACXX.1_2.fastq
+  location: HWI-ST1027_129_D0THKACXX.1_2.fastq
 group_id: arvados_tutorial
 sample_id: HWI-ST1027_129
 PL: illumina
diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input.yml b/doc/user/cwl/bwa-mem/bwa-mem-input.yml
index 8e29b60ecd..af248c9965 100755
--- a/doc/user/cwl/bwa-mem/bwa-mem-input.yml
+++ b/doc/user/cwl/bwa-mem/bwa-mem-input.yml
@@ -2,13 +2,13 @@
 cwl:tool: bwa-mem.cwl
 reference:
   class: File
-  path: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
+  location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
 read_p1:
   class: File
-  path: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq
+  location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq
 read_p2:
   class: File
-  path: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq
+  location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq
 group_id: arvados_tutorial
 sample_id: HWI-ST1027_129
 PL: illumina
diff --git a/doc/user/cwl/bwa-mem/bwa-mem-template.yml b/doc/user/cwl/bwa-mem/bwa-mem-template.yml
index bc59427cd1..448f765c86 100755
--- a/doc/user/cwl/bwa-mem/bwa-mem-template.yml
+++ b/doc/user/cwl/bwa-mem/bwa-mem-template.yml
@@ -1,4 +1,4 @@
 reference:
   class: File
-  path: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
+  location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
 PL: illumina
diff --git a/doc/user/cwl/bwa-mem/bwa-mem.cwl b/doc/user/cwl/bwa-mem/bwa-mem.cwl
index 1a16a3dcd3..ba3b6a0e89 100755
--- a/doc/user/cwl/bwa-mem/bwa-mem.cwl
+++ b/doc/user/cwl/bwa-mem/bwa-mem.cwl
@@ -1,12 +1,10 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: draft-3
+cwlVersion: v1.0
 class: CommandLineTool
 
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: biodckr/bwa
-requirements:
-  - class: InlineJavascriptRequirement
 
 baseCommand: [bwa, mem]
 
@@ -15,38 +13,33 @@ arguments:
   - {prefix: "-R", valueFrom: "@RG\tID:$(inputs.group_id)\tPL:$(inputs.PL)\tSM:$(inputs.sample_id)"}
 
 inputs:
-  - id: reference
+  reference:
     type: File
     inputBinding:
       position: 1
-      valueFrom: $(self.path.match(/(.*)\.[^.]+$/)[1])
+      valueFrom: $(self.dirname)/$(self.nameroot)
     secondaryFiles:
       - ^.ann
       - ^.amb
       - ^.pac
       - ^.sa
-    description: The index files produced by `bwa index`
-  - id: read_p1
+    doc: The index files produced by `bwa index`
+  read_p1:
     type: File
     inputBinding:
       position: 2
-    description: The reads, in fastq format.
-  - id: read_p2
-    type: ["null", File]
+    doc: The reads, in fastq format.
+  read_p2:
+    type: File?
     inputBinding:
       position: 3
-    description:  For mate paired reads, the second file (optional).
-  - id: group_id
-    type: string
-  - id: sample_id
-    type: string
-  - id: PL
-    type: string
+    doc:  For mate paired reads, the second file (optional).
+  group_id: string
+  sample_id: string
+  PL: string
 
-stdout: $(inputs.read_p1.path.match(/\/([^/]+)\.[^/.]+$/)[1] + ".sam")
+stdout: $(inputs.read_p1.nameroot).sam
 
 outputs:
-  - id: aligned_sam
-    type: File
-    outputBinding:
-      glob: $(inputs.read_p1.path.match(/\/([^/]+)\.[^/.]+$/)[1] + ".sam")
+  aligned_sam:
+    type: stdout
-- 
2.30.2