+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
{
"name": "Tutorial align using bwa mem and SortSam",
"components": {
"repository": "arvados",
"script_parameters": {
"command": [
- "bwa",
+ "$(dir $(bwa_collection))/bwa",
"mem",
"-t",
"$(node.cores)",
"-R",
- "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id",
+ "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
"$(glob $(dir $(reference_collection))/*.fasta)",
"$(glob $(dir $(sample))/*_1.fastq)",
"$(glob $(dir $(sample))/*_2.fastq)"
"required": true,
"dataclass": "Collection"
},
+ "bwa_collection": {
+ "required": true,
+ "dataclass": "Collection",
+ "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+ },
"sample": {
"required": true,
"dataclass": "Collection"
},
- "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
},
"runtime_constraints": {
- "docker_image": "arvados/jobs-java-bwa-samtools"
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
}
},
"SortSam": {
}
},
"runtime_constraints": {
- "docker_image": "arvados/jobs-java-bwa-samtools"
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
}
}
}