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| author | Peter Amstutz | 2020-04-21 17:09:16 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-21 17:09:16 -0400 |
| commit | ce696b41b3476891ecb05185d64c289b140a73af (patch) | |
| tree | 466dfc19d583aedb44f366ddacc6fa8e0b7a890e | |
| parent | 61726edb9293fe529e6efbe5bb6f1cc953bb3c4e (diff) | |
| download | bh20-seq-resource-ce696b41b3476891ecb05185d64c289b140a73af.tar.gz bh20-seq-resource-ce696b41b3476891ecb05185d64c289b140a73af.tar.lz bh20-seq-resource-ce696b41b3476891ecb05185d64c289b140a73af.zip | |
Increase ram requirement for minimap2
Add --kickoff to immediately start an analysis workflow.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| -rw-r--r-- | bh20seqanalyzer/main.py | 14 | ||||
| -rw-r--r-- | workflows/pangenome-generate/minimap2.cwl | 2 |
2 files changed, 14 insertions, 2 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 193a268..8d0f562 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -214,14 +214,26 @@ def main(): parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='') parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') + parser.add_argument('--kickoff', action="store_true") args = parser.parse_args() api = arvados.api() - logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project)) + schema_ref = upload_schema(api, args.workflow_def_project) + if args.kickoff: + logging.info("Starting a single analysis run") + start_pangenome_analysis(api, + args.pangenome_analysis_project, + args.pangenome_workflow_uuid, + args.validated_project, + schema_ref) + return + + logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project)) + while True: move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project) diff --git a/workflows/pangenome-generate/minimap2.cwl b/workflows/pangenome-generate/minimap2.cwl index bf19ef7..42d1dce 100644 --- a/workflows/pangenome-generate/minimap2.cwl +++ b/workflows/pangenome-generate/minimap2.cwl @@ -12,7 +12,7 @@ hints: ResourceRequirement: coresMin: 8 coresMax: 32 - ramMin: $(7 * 1024) + ramMin: $(9 * 1024) outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20)) stdout: $(inputs.readsFA.nameroot).paf baseCommand: minimap2 |