Merge branch '15397-remove-obsolete-apis'

[arvados.git] / doc / user / cwl / bwa-mem / bwa-mem.cwl

diff --git a/doc/user/cwl/bwa-mem/bwa-mem.cwl b/doc/user/cwl/bwa-mem/bwa-mem.cwl
index 1a16a3dcd3297cf562714852564fd2eb6d7a13c4..018867c83e29bdf04bb6d54173e86f059c192d0c 100755 (executable)
--- a/doc/user/cwl/bwa-mem/bwa-mem.cwl
+++ b/doc/user/cwl/bwa-mem/bwa-mem.cwl
@@ -1,52 +1,49 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: draft-3
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: CC-BY-SA-3.0
+
+cwlVersion: v1.0
 class: CommandLineTool
 
 hints:
-  - class: DockerRequirement
-    dockerPull: biodckr/bwa
-requirements:
-  - class: InlineJavascriptRequirement
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/bwa:0.7.17--ha92aebf_3
 
 baseCommand: [bwa, mem]
 
 arguments:
   - {prefix: "-t", valueFrom: $(runtime.cores)}
-  - {prefix: "-R", valueFrom: "@RG\tID:$(inputs.group_id)\tPL:$(inputs.PL)\tSM:$(inputs.sample_id)"}
+  - {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