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| author | Peter Amstutz | 2020-05-26 17:30:30 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-05-26 18:12:23 -0400 |
| commit | 7a96d0b1b15ab28fe3a618db35364891ab5d0328 (patch) | |
| tree | 570532d2cc4c490175a4042d7bfabaad5120312d /bh20seqanalyzer | |
| parent | 30f3f8b0e9efbc954518fc8ea621b53c9591c83a (diff) | |
| download | bh20-seq-resource-7a96d0b1b15ab28fe3a618db35364891ab5d0328.tar.gz bh20-seq-resource-7a96d0b1b15ab28fe3a618db35364891ab5d0328.tar.lz bh20-seq-resource-7a96d0b1b15ab28fe3a618db35364891ab5d0328.zip | |
Can have list of sequence labels to exclude from combined fasta
refs #68
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20seqanalyzer')
| -rw-r--r-- | bh20seqanalyzer/main.py | 15 |
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, |