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3dc433d
feat: new `unified_pipeline` dag after pis, pts, etl changes
ireneisdoomed Nov 10, 2025
3abb528
Merge branch 'dev' of https://github.com/opentargets/orchestration in…
ireneisdoomed Nov 10, 2025
259d09c
chore: update susie credible sets path
ireneisdoomed Nov 10, 2025
8af169e
chore: review common dependencies
ireneisdoomed Nov 10, 2025
ae1370d
chore: update gentropy version
ireneisdoomed Nov 10, 2025
1a8416e
chore: resize airflow dev instance from `n1-standard-16` to `n1-stand…
ireneisdoomed Nov 10, 2025
99e4384
fix: rename etl_evidence to pts_evidence_postprocess
ireneisdoomed Nov 11, 2025
ee1cbea
chore: rename pts_evidence_postprocess to pts_validate_evidence for c…
ireneisdoomed Nov 11, 2025
06ea552
chore: remove etl evidence config and accomodate changes
ireneisdoomed Nov 11, 2025
5645213
fix: gold standard path
ireneisdoomed Nov 11, 2025
f7fcac8
update pis and pts configs
javfg Nov 11, 2025
c38595b
fix: paths
ireneisdoomed Nov 12, 2025
432069b
fix: change openai token secrets
javfg Nov 12, 2025
e196d2e
fix: add missing deps for ontoma
javfg Nov 12, 2025
3e57a61
chore: add enhancer to gene pis step and fix gnomad version
ireneisdoomed Nov 12, 2025
ba8ae6b
chore: add enhancer to gene pis step and fix gnomad version
ireneisdoomed Nov 12, 2025
211b3d8
chore: uncomment steps
ireneisdoomed Nov 12, 2025
cf4b21d
fix: curation paths and update path
ireneisdoomed Nov 12, 2025
43d0825
fix: curation paths
ireneisdoomed Nov 12, 2025
836388c
fix: indentation
ireneisdoomed Nov 12, 2025
137837a
fix: name inner file
ireneisdoomed Nov 12, 2025
43f67be
chore: set colocalisation steps
ireneisdoomed Nov 12, 2025
0696d9c
chore: clean gentropy step deps
ireneisdoomed Nov 12, 2025
6c553b6
fix(pts): drop gnomad transformation
ireneisdoomed Nov 12, 2025
3c6bbd6
fix: add pts_ontoma
ireneisdoomed Nov 12, 2025
fb8299a
fix: add pts_target_gene_essentiality pts_target_safety for etl_target
ireneisdoomed Nov 12, 2025
95b1db4
fix: drop runtime spark-nlp jar downloads and use package from pip
ireneisdoomed Nov 13, 2025
44c499a
fix: cancer_biomarkers deps
ireneisdoomed Nov 13, 2025
da97446
chore: update pis, pts versions
ireneisdoomed Nov 13, 2025
ac37467
chore: fix multiple configs
ireneisdoomed Nov 14, 2025
146c333
chore: fix multiple configs
ireneisdoomed Nov 14, 2025
44f3201
feat: add evidence post process
ireneisdoomed Nov 16, 2025
4a573e4
feat: update evidence post process
ireneisdoomed Nov 16, 2025
970ff4f
chore: fixes
ireneisdoomed Nov 16, 2025
e2a42a1
chore(evidence_cosmic): input is not gzipped
ireneisdoomed Nov 16, 2025
63e816b
chore: more fixes
ireneisdoomed Nov 17, 2025
49a7e7f
chore: merge
ireneisdoomed Nov 17, 2025
c77548e
fix: pis version with openfda fix
ireneisdoomed Nov 17, 2025
ef67246
fix: l2g_prediction output path
ireneisdoomed Nov 17, 2025
a3caaca
fix[pts]: pharmacogenetics config for the coding_variant
d0choa Nov 17, 2025
030e642
fix[pis]: expression step configuration
d0choa Nov 17, 2025
e36156f
fix[pts]: expression step configuration
d0choa Nov 17, 2025
4b45dc4
feat(pis): update panelapp step
ireneisdoomed Nov 18, 2025
0d2eceb
feat(pts): update panelapp step
ireneisdoomed Nov 18, 2025
5a1abb1
fix: typo
ireneisdoomed Nov 18, 2025
64ff6c5
fix(reactome): input file is json
ireneisdoomed Nov 18, 2025
e2c7dfa
feat(pis): add intogen step
ireneisdoomed Nov 18, 2025
593463c
feat(pts): add intogen steps
ireneisdoomed Nov 18, 2025
5a21c9d
fix: typo
ireneisdoomed Nov 18, 2025
c964ca4
fix(pis): typo
ireneisdoomed Nov 18, 2025
3e8e8c8
fix(pts): typo
ireneisdoomed Nov 18, 2025
2c51a3b
fix orphanet direction on target
DSuveges Nov 19, 2025
cf0bf6d
chore: update pis, pts
ireneisdoomed Nov 19, 2025
1cdabb7
fix(pis): copy filtered e2g (score>.6)
ireneisdoomed Nov 20, 2025
c5b3f47
fix(etl): correct `evidences` def in `association_otf`
ireneisdoomed Nov 20, 2025
2087aaf
chore: test timeseries run
ireneisdoomed Nov 20, 2025
1bcf1f4
chore: test 2 timeseries run
ireneisdoomed Nov 20, 2025
c5f4758
fix: correct `known_drug` evidence path
ireneisdoomed Nov 21, 2025
8b18061
chore: update pts to 25.3.1-dev.17 with impc fix
ireneisdoomed Nov 21, 2025
d1e657a
chore: update pts to 25.3.1-dev.18 with evidence validation
ireneisdoomed Nov 21, 2025
60daaf4
fix: correct evidence_postprocess_europepmc input
ireneisdoomed Nov 21, 2025
05a89b1
fix: amend impc threshold from 0.41 to 41
ireneisdoomed Nov 23, 2025
2da17f0
chore: update burden
ireneisdoomed Nov 23, 2025
5a4cbdf
Change keep_only_essentials setting to false
DSuveges Nov 24, 2025
136988c
fix(pts): include evidence for non essential genes
ireneisdoomed Nov 24, 2025
1574194
Merge branch 'il-2512-poc' of https://github.com/opentargets/orchestr…
ireneisdoomed Nov 24, 2025
5569e06
Unifying direction of effect expressions
DSuveges Nov 25, 2025
6a587f6
make timeseries ppp only
javfg Nov 26, 2025
3cf7cca
increase coloc partitions
javfg Nov 26, 2025
3986357
fix(etl): correct input format for `search`
ireneisdoomed Nov 26, 2025
68cc247
fix(etl): only evidence needs to be an object in `search`
ireneisdoomed Nov 26, 2025
36e3ca7
fix(etl): only evidence needs to be an object in `search`
ireneisdoomed Nov 26, 2025
e915ccf
fix: re-wiring variant index generation (#157)
DSuveges Nov 26, 2025
fb6d020
chore: update pts to include harmonisation
ireneisdoomed Nov 26, 2025
da55f3a
chore: test reverting target input
ireneisdoomed Nov 26, 2025
e994f98
fix: typo in `target.inputs.gene_essentiality`
ireneisdoomed Nov 26, 2025
9404a5c
feat(pis): download hgnc json
ireneisdoomed Nov 26, 2025
5afc413
fix: typo
ireneisdoomed Nov 26, 2025
163e446
chore: update etl version with hgnc fix
ireneisdoomed Nov 26, 2025
b41bf92
chore: update gentropy version
ireneisdoomed Nov 26, 2025
e239d55
chore: config for second run
ireneisdoomed Nov 27, 2025
e2d9fcd
Merge branch 'dev' of https://github.com/opentargets/orchestration in…
ireneisdoomed Nov 27, 2025
7eb651a
fix: diff operator doesnt use step group
ireneisdoomed Nov 27, 2025
4fa302b
fix(pts): define target and disease dependencies for evidence postpro…
ireneisdoomed Nov 27, 2025
d0f55c1
fix: step deps
ireneisdoomed Nov 27, 2025
823fed9
fix: cosmic input is compressed
ireneisdoomed Nov 28, 2025
16e8c63
fix(etl): target reference path
ireneisdoomed Nov 28, 2025
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2 changes: 1 addition & 1 deletion deployment/main.tf
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ data "external" "user" {

resource "google_compute_instance" "up_airflow_dev_vm" {
name = "up-airflow-dev-${random_string.up_airflow_dev_vm.result}"
machine_type = "n1-standard-16"
machine_type = "n1-standard-32"
metadata = {
orchestration_git_branch = var.orchestration_git_branch
}
Expand Down
44 changes: 22 additions & 22 deletions docs/credible_set_qc/credible_set_qc.svg
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48 changes: 24 additions & 24 deletions docs/datasources/eqtl_catalogue_data/eqtl_catalogue_ingestion.svg
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