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authorLLTommy2020-04-23 20:18:36 +0200
committerGitHub2020-04-23 20:18:36 +0200
commit7049cd5d29acd601ccbbc9d04f001b84a51e9bd5 (patch)
tree34a1254d81c2e526427fedb1deaa9f8441e8b260 /bh20seqanalyzer/main.py
parentf38b9c6f22b82327df9648938a5a4bcf863d8c41 (diff)
parentc7612e7eda5cd38bfbb2d293bebf732893a41b6c (diff)
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Merge branch 'master' into patch-3
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)