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-rw-r--r--bh20seqanalyzer/main.py15
1 files changed, 12 insertions, 3 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 28b5e31..31ad4c4 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -125,7 +125,8 @@ def start_pangenome_analysis(api,
analysis_project,
pangenome_workflow_uuid,
validated_project,
- schema_ref):
+ schema_ref,
+ exclude_list):
validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]])
inputobj = {
"inputReads": [],
@@ -134,6 +135,10 @@ def start_pangenome_analysis(api,
"metadataSchema": {
"class": "File",
"location": schema_ref
+ },
+ "exclude": {
+ "class": "File",
+ "location": exclude_list
}
}
validated.sort(key=lambda v: v["portable_data_hash"])
@@ -213,6 +218,8 @@ def main():
parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='')
+ parser.add_argument('--exclude-list', type=str, default='keep:lugli-4zz18-tzzhcm6hrf8ci8d/exclude.txt', 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()
@@ -229,7 +236,8 @@ def main():
args.pangenome_analysis_project,
args.pangenome_workflow_uuid,
args.validated_project,
- schema_ref)
+ schema_ref,
+ args.exclude_list)
return
logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
@@ -250,7 +258,8 @@ def main():
args.pangenome_analysis_project,
args.pangenome_workflow_uuid,
args.validated_project,
- schema_ref)
+ schema_ref,
+ args.exclude_list)
copy_most_recent_result(api,
args.pangenome_analysis_project,