+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
{
"name":"run-command example pipeline",
"components":{
- "bwa-mem": {
+ "bwa-mem": {
"script": "run-command",
"script_version": "master",
"repository": "arvados",
"script_parameters": {
"command": [
- "bwa",
+ "$(dir $(bwa_collection))/bwa",
"mem",
"-t",
"$(node.cores)",
+ "-R",
+ "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
"$(glob $(dir $(reference_collection))/*.fasta)",
"$(glob $(dir $(sample))/*_1.fastq)",
"$(glob $(dir $(sample))/*_2.fastq)"
],
- "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
"reference_collection": {
"required": true,
"dataclass": "Collection"
},
+ "bwa_collection": {
+ "required": true,
+ "dataclass": "Collection",
+ "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+ },
"sample": {
"required": true,
"dataclass": "Collection"
- }
+ },
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
}
}
}