2 "name": "Tutorial align using bwa mem and SortSam",
5 "script": "run-command",
6 "script_version": "master",
7 "repository": "arvados",
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 $(sample))/*_2.fastq)"
20 "reference_collection": {
22 "dataclass": "Collection"
26 "dataclass": "Collection"
28 "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
30 "runtime_constraints": {
31 "docker_image": "arvados/jobs-java-bwa-samtools"
35 "script": "run-command",
36 "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
37 "repository": "arvados",
38 "script_parameters": {
42 "-Djava.io.tmpdir=$(tmpdir)",
44 "$(dir $(picard))/SortSam.jar",
46 "SORT_ORDER=coordinate",
47 "VALIDATION_STRINGENCY=LENIENT",
48 "INPUT=$(glob $(dir $(input))/*.sam)",
49 "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
52 "output_of": "bwa-mem"
56 "dataclass": "Collection",
57 "default": "88447c464574ad7f79e551070043f9a9+1970"
60 "runtime_constraints": {
61 "docker_image": "arvados/jobs-java-bwa-samtools"