2 "name": "Tutorial align using bwa mem and SortSam",
5 "script": "run-command",
6 "script_version": "master",
7 "repository": "arvados",
10 "$(dir $(bwa_collection))/bwa",
15 "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
16 "$(glob $(dir $(reference_collection))/*.fasta)",
17 "$(glob $(dir $(sample))/*_1.fastq)",
18 "$(glob $(dir $(sample))/*_2.fastq)"
20 "reference_collection": {
22 "dataclass": "Collection"
26 "dataclass": "Collection",
27 "default": "39c6f22d40001074f4200a72559ae7eb+5745"
31 "dataclass": "Collection"
33 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
35 "runtime_constraints": {
36 "docker_image": "bcosc/arv-base-java",
37 "arvados_sdk_version": "master"
41 "script": "run-command",
42 "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
43 "repository": "arvados",
44 "script_parameters": {
48 "-Djava.io.tmpdir=$(tmpdir)",
50 "$(dir $(picard))/SortSam.jar",
52 "SORT_ORDER=coordinate",
53 "VALIDATION_STRINGENCY=LENIENT",
54 "INPUT=$(glob $(dir $(input))/*.sam)",
55 "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
58 "output_of": "bwa-mem"
62 "dataclass": "Collection",
63 "default": "88447c464574ad7f79e551070043f9a9+1970"
66 "runtime_constraints": {
67 "docker_image": "bcosc/arv-base-java",
68 "arvados_sdk_version": "master"