2 Copyright (C) The Arvados Authors. All rights reserved.
4 SPDX-License-Identifier: CC-BY-SA-3.0
8 "name": "Tutorial align using bwa mem and SortSam",
11 "script": "run-command",
12 "script_version": "master",
13 "repository": "arvados",
14 "script_parameters": {
16 "$(dir $(bwa_collection))/bwa",
21 "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
22 "$(glob $(dir $(reference_collection))/*.fasta)",
23 "$(glob $(dir $(sample))/*_1.fastq)",
24 "$(glob $(dir $(sample))/*_2.fastq)"
26 "reference_collection": {
28 "dataclass": "Collection"
32 "dataclass": "Collection",
33 "default": "39c6f22d40001074f4200a72559ae7eb+5745"
37 "dataclass": "Collection"
39 "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
41 "runtime_constraints": {
42 "docker_image": "bcosc/arv-base-java",
43 "arvados_sdk_version": "master"
47 "script": "run-command",
48 "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
49 "repository": "arvados",
50 "script_parameters": {
54 "-Djava.io.tmpdir=$(tmpdir)",
56 "$(dir $(picard))/SortSam.jar",
58 "SORT_ORDER=coordinate",
59 "VALIDATION_STRINGENCY=LENIENT",
60 "INPUT=$(glob $(dir $(input))/*.sam)",
61 "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
64 "output_of": "bwa-mem"
68 "dataclass": "Collection",
69 "default": "88447c464574ad7f79e551070043f9a9+1970"
72 "runtime_constraints": {
73 "docker_image": "bcosc/arv-base-java",
74 "arvados_sdk_version": "master"