+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
{
"name":"run-command example pipeline",
"components":{
{
"foreach": "read_pair",
"command": "$(read_pair)"
- },
- "$(glob $(dir $(sample))/*_1.fastq)",
- "$(glob $(dir $(sample))/*_2.fastq)"
+ }
],
"task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
"task.foreach": ["sample_subdir", "read_pair"],
- "reference_collection": "2463fa9efeb75e099685528b3b9071e0+438",
- "samples": "df45f4be79668b6d3d974e24f78e766f+149",
- "sample_subdir": "$(dir $(samples))",
- "read_pair": {
- "group": "sample_subdir",
- "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
- }
- }
- }
- }
-}
-
-
"reference_collection": {
"required": true,
"dataclass": "Collection"
"sample": {
"required": true,
"dataclass": "Collection"
+ },
+ "sample_subdir": "$(dir $(sample))",
+ "read_pair": {
+ "value": {
+ "group": "sample_subdir",
+ "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
+ }
}
+ }
+ }
+ }
+}