9369: arvados-cwl-runner documentation and examples, add deprecation notices to pipel...

[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
new file mode 100755 (executable)
index 0000000..1a16a3d
--- /dev/null
+++ b/doc/user/cwl/bwa-mem/bwa-mem.cwl
@@ -0,0 +1,52 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: draft-3
+class: CommandLineTool
+
+hints:
+  - class: DockerRequirement
+    dockerPull: biodckr/bwa
+requirements:
+  - class: InlineJavascriptRequirement
+
+baseCommand: [bwa, mem]
+
+arguments:
+  - {prefix: "-t", valueFrom: $(runtime.cores)}
+  - {prefix: "-R", valueFrom: "@RG\tID:$(inputs.group_id)\tPL:$(inputs.PL)\tSM:$(inputs.sample_id)"}
+
+inputs:
+  - id: reference
+    type: File
+    inputBinding:
+      position: 1
+      valueFrom: $(self.path.match(/(.*)\.[^.]+$/)[1])
+    secondaryFiles:
+      - ^.ann
+      - ^.amb
+      - ^.pac
+      - ^.sa
+    description: The index files produced by `bwa index`
+  - id: read_p1
+    type: File
+    inputBinding:
+      position: 2
+    description: The reads, in fastq format.
+  - id: read_p2
+    type: ["null", 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
+
+stdout: $(inputs.read_p1.path.match(/\/([^/]+)\.[^/.]+$/)[1] + ".sam")
+
+outputs:
+  - id: aligned_sam
+    type: File
+    outputBinding:
+      glob: $(inputs.read_p1.path.match(/\/([^/]+)\.[^/.]+$/)[1] + ".sam")