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authorPeter Amstutz2020-04-21 17:09:16 -0400
committerPeter Amstutz2020-04-21 17:09:16 -0400
commitce696b41b3476891ecb05185d64c289b140a73af (patch)
tree466dfc19d583aedb44f366ddacc6fa8e0b7a890e /bh20seqanalyzer
parent61726edb9293fe529e6efbe5bb6f1cc953bb3c4e (diff)
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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>
Diffstat (limited to 'bh20seqanalyzer')
-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)