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| author | Peter Amstutz | 2020-08-19 15:19:07 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | b3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch) | |
| tree | 92adcacbd208546bf3f063e6c25765e660972244 /bh20seqanalyzer/main.py | |
| parent | 592c921a3223c03d8a22f7a852641ac5d753fb31 (diff) | |
| download | bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.gz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.lz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.zip | |
Consolidate steps to scale graph generation workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20seqanalyzer/main.py')
| -rw-r--r-- | bh20seqanalyzer/main.py | 21 |
1 files changed, 3 insertions, 18 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index ad3c3d7..13efbeb 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -181,13 +181,7 @@ class SeqAnalyzer: if self.schema_ref is None: self.upload_schema() - validated = arvados.util.list_all(self.api.collections().list, filters=[ - ["owner_uuid", "=", self.validated_project], - ["properties.status", "=", "validated"]]) inputobj = { - "inputReads": [], - "metadata": [], - "subjects": [], "metadataSchema": { "class": "File", "location": self.schema_ref @@ -195,19 +189,10 @@ class SeqAnalyzer: "exclude": { "class": "File", "location": self.exclude_list - } + }, + "src_project": self.validated_project } - validated.sort(key=lambda v: v["portable_data_hash"]) - for v in validated: - inputobj["inputReads"].append({ - "class": "File", - "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] - }) - inputobj["metadata"].append({ - "class": "File", - "location": "keep:%s/metadata.yaml" % v["portable_data_hash"] - }) - inputobj["subjects"].append("http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % v["portable_data_hash"]) + self.run_workflow(self.pangenome_analysis_project, self.pangenome_workflow_uuid, "Pangenome analysis", inputobj) |