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authorlltommy2020-04-22 18:37:35 +0200
committerlltommy2020-04-22 18:37:35 +0200
commit5582ed4f4bd6bd5b03d20a0c88dc7fa27d2d5cde (patch)
tree466dfc19d583aedb44f366ddacc6fa8e0b7a890e /bh20seqanalyzer/main.py
parentb34531de1f49e4faa82a9c350f0c5d4169ccfeb4 (diff)
parentce696b41b3476891ecb05185d64c289b140a73af (diff)
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Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'bh20seqanalyzer/main.py')
-rw-r--r--bh20seqanalyzer/main.py14
1 files changed, 13 insertions, 1 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)