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

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

diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input.yml b/doc/user/cwl/bwa-mem/bwa-mem-input.yml
new file mode 100755 (executable)
index 0000000..8e29b60
--- /dev/null
+++ b/doc/user/cwl/bwa-mem/bwa-mem-input.yml
@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwl:tool: bwa-mem.cwl
+reference:
+  class: File
+  path: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
+read_p1:
+  class: File
+  path: 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
+group_id: arvados_tutorial
+sample_id: HWI-ST1027_129
+PL: illumina