From 6cdfd69fc3722e1851bea02c6675337952d34e26 Mon Sep 17 00:00:00 2001 From: Javier Ferrer Date: Tue, 21 Jan 2025 10:28:58 +0000 Subject: [PATCH] New config fixes --- config.yaml | 35 ++++++++++++++++------------------- 1 file changed, 16 insertions(+), 19 deletions(-) diff --git a/config.yaml b/config.yaml index 879c197..1ede7d6 100644 --- a/config.yaml +++ b/config.yaml @@ -5,7 +5,7 @@ pool: 8 scratchpad: chembl_version: '34' - efo_version: v3.70.0 + efo_version: '3.70.0' ensembl_version: '113' steps: @@ -17,12 +17,12 @@ steps: source: https://github.com/obophenotype/uberon/releases/latest/download/uberon.json destination: biosample/uberon.json - name: download efo - source: https://github.com/EBISPOT/efo/releases/download/${efo_version}/efo.json + source: https://github.com/EBISPOT/efo/releases/download/v${efo_version}/efo.json destination: biosample/efo.json disease: - name: download efo otar_slim - source: https://github.com/EBISPOT/efo/releases/download/${efo_version}/efo_otar_slim.json + source: https://github.com/EBISPOT/efo/releases/download/v${efo_version}/efo_otar_slim.json destination: disease/efo_otar_slim.json - name: download hpo source: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/v2021-10-10/hp.json @@ -43,7 +43,7 @@ steps: destination: drug/drugbank.csv.gz - name: elasticsearch chembl drug indication url: https://www.ebi.ac.uk/chembl/elk/es - destination: chembl-inputs/chembl_${chembl_version}_drug_indication.jsonl + destination: drug/chembl_drug_indication.jsonl index: chembl_${chembl_version}_drug_indication fields: - _metadata @@ -53,7 +53,7 @@ steps: - indication_refs - name: elasticsearch chembl drug warning url: https://www.ebi.ac.uk/chembl/elk/es - destination: chembl-inputs/chembl_${chembl_version}_drug_warning.jsonl + destination: drug/chembl_drug_warning.jsonl index: chembl_${chembl_version}_drug_warning fields: - _metadata @@ -71,7 +71,7 @@ steps: - warning_year - name: elasticsearch chembl mechanism of action url: https://www.ebi.ac.uk/chembl/elk/es - destination: chembl-inputs/chembl_${chembl_version}_mechanism.jsonl + destination: drug/chembl_mechanism.jsonl index: chembl_${chembl_version}_mechanism fields: - _metadata @@ -84,7 +84,7 @@ steps: - parent_molecule_chembl_id - name: elasticsearch chembl molecule url: https://www.ebi.ac.uk/chembl/elk/es - destination: chembl-inputs/chembl_${chembl_version}_molecule.jsonl + destination: drug/chembl_molecule.jsonl index: chembl_${chembl_version}_molecule fields: - molecule_chembl_id @@ -101,7 +101,7 @@ steps: - molecule_structures - name: elasticsearch chembl target url: https://www.ebi.ac.uk/chembl/elk/es - destination: chembl-inputs/chembl_${chembl_version}_target.jsonl + destination: drug/chembl_target.jsonl index: chembl_${chembl_version}_target fields: - _metadata @@ -190,13 +190,10 @@ steps: destination: expression/expression_hierarchy_curation.tsv - name: download tissue translation map source: https://raw.githubusercontent.com/opentargets/expression_hierarchy/master/process/map_with_efos.json - destination: expression/map_with_efos.jsonl + destination: expression/map_with_efos.json - name: download normal tissues source: https://www.proteinatlas.org/download/tsv/normal_tissue.tsv.zip destination: expression/normal_tissue.tsv.zip - - name: download_latest baseline expression - source: gs://otar000-evidence_input/BaselineExpression/json - destination: expression/baseline_expression.json.gz - name: download_latest baseline expression binned source: gs://atlas_baseline_expression/baseline_expression_binned destination: expression/baseline_expression_binned.tsv @@ -215,19 +212,19 @@ steps: interaction: - name: download ensembl interactions grch38 source: https://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${ensembl_version}.chr.gtf.gz - destination: interactions-inputs/Homo_sapiens.GRCh38.chr.gtf.gz + destination: interaction/Homo_sapiens.GRCh38.chr.gtf.gz - name: download human 9606 idmapping source: https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz - destination: interactions-inputs/HUMAN_9606_idmapping.dat.gz + destination: interaction/HUMAN_9606_idmapping.dat.gz - name: download intact interactors source: https://ftp.ebi.ac.uk/pub/databases/intact/various/ot_graphdb/current/data/interactor_pair_interactions.json - destination: interactions-inputs/intact-interactors.json + destination: interaction/intact-interactors.json - name: download rna central source: https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/ensembl.tsv - destination: interactions-inputs/rna_central_ensembl.tsv + destination: interaction/rna_central_ensembl.tsv - name: download_latest string interactions source: gs://otar001-core/stringInteractions - destination: interactions-inputs/string-interactions.txt.gz + destination: interaction/string-interactions.txt.gz l2g_prediction: - name: download model @@ -237,7 +234,7 @@ steps: literature: - name: download literature source: https://ftp.ebi.ac.uk/pub/databases/pmc/DOI/PMID_PMCID_DOI.csv.gz - destination: literature-inputs/PMID_PMCID_DOI.csv.gz + destination: literature/PMID_PMCID_DOI.csv.gz openfda: - name: download blacklisted events @@ -309,7 +306,7 @@ steps: destination: target/homologue/homologies/ncrna-${species}.tsv - name: elasticsearch chembl targets url: https://www.ebi.ac.uk/chembl/elk/es - destination: chembl-inputs/chembl_${chembl_version}_target.jsonl + destination: target/chembl/chembl_target.jsonl index: chembl_${chembl_version}_target fields: - _metadata