14322: Add additional example input files

* with uuids
* with both portable data hashes and uuids

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml b/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml
new file mode 100755 (executable)
index 0000000..8863cba
--- /dev/null
+++ b/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml
@@ -0,0 +1,27 @@
+#!/usr/bin/env cwl-runner
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: CC-BY-SA-3.0
+
+# Example input file using UUIDs to reference input collections. These
+# will be resolved to content addresses before running the workflow.
+
+$namespaces:
+  arv: 'http://arvados.org/cwl#'
+
+cwl:tool: bwa-mem.cwl
+reference:
+  class: File
+  location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
+  arv:collectionUUID: qr1hi-4zz18-pwid4w22a40jp8l
+read_p1:
+  class: File
+  location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq
+  arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0
+read_p2:
+  class: File
+  location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq
+  arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0
+group_id: arvados_tutorial
+sample_id: HWI-ST1027_129
+PL: illumina

diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml b/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml
new file mode 100755 (executable)
index 0000000..7e71e95
--- /dev/null
+++ b/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml
@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: CC-BY-SA-3.0
+
+# Example input file using UUIDs to reference input collections. These
+# will be resolved to content addresses before running the workflow.
+
+cwl:tool: bwa-mem.cwl
+reference:
+  class: File
+  location: keep:qr1hi-4zz18-pwid4w22a40jp8l/19.fasta.bwt
+read_p1:
+  class: File
+  location: keep:qr1hi-4zz18-h615rgfmqt3wje0/HWI-ST1027_129_D0THKACXX.1_1.fastq
+read_p2:
+  class: File
+  location: keep:qr1hi-4zz18-h615rgfmqt3wje0/HWI-ST1027_129_D0THKACXX.1_2.fastq
+group_id: arvados_tutorial
+sample_id: HWI-ST1027_129
+PL: illumina