- "name": "Tutorial align using bwa mem and SortSam",
- "components": {
- "bwa-mem": {
- "script": "run-command",
- "script_version": "master",
- "repository": "arvados",
- "script_parameters": {
- "command": [
- "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 $(sample))/*_2.fastq)"
- ],
- "reference_collection": {
- "required": true,
- "dataclass": "Collection"
+ "name": "Tutorial align using bwa mem and SortSam",
+ "components": {
+ "bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "$(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 $(sample))/*_2.fastq)"
+ ],
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "bwa_collection": {
+ "required": true,
+ "dataclass": "Collection",
+ "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+ },
+ "sample": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+ },
+ "runtime_constraints": {
+ "docker_image": "bcosc/arv-base-java",
+ "arvados_sdk_version": "master"
+ }