aboutsummaryrefslogtreecommitdiff
path: root/bh20seqanalyzer/main.py
diff options
context:
space:
mode:
authorPeter Amstutz2020-08-19 15:19:07 -0400
committerPeter Amstutz2020-08-19 16:31:38 -0400
commitb3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch)
tree92adcacbd208546bf3f063e6c25765e660972244 /bh20seqanalyzer/main.py
parent592c921a3223c03d8a22f7a852641ac5d753fb31 (diff)
downloadbh20-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.py21
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)