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authorPeter Amstutz2020-04-21 17:09:16 -0400
committerPeter Amstutz2020-04-21 17:09:16 -0400
commitce696b41b3476891ecb05185d64c289b140a73af (patch)
tree466dfc19d583aedb44f366ddacc6fa8e0b7a890e
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>
-rw-r--r--bh20seqanalyzer/main.py14
-rw-r--r--workflows/pangenome-generate/minimap2.cwl2
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