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interval index dag #120

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interval index dag #120

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1843ab7
feat: dag config for interval index
xyg123 Mar 27, 2025
91057a3
fix: interval output path
xyg123 Mar 27, 2025
da59012
Merge branch 'dev' into xg1_interval_index
project-defiant Apr 4, 2025
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16 changes: 16 additions & 0 deletions src/ot_orchestration/dags/config/genetics_etl.yaml
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Expand Up @@ -183,6 +183,22 @@ nodes:
+step.session.extended_spark_conf: "{spark.executor.memory: '25g', spark.executor.memoryOverhead: '1g', spark.executor.cores: '4'}"
step.session.write_mode: overwrite

- id: interval_index
prerequisites:
- variant_index
params:
step: interval_index
step.variant_index_path: '{release_dir}/variant_index'
step.target_index_path: '{target_index}'
step.interval_sources: {}
+step.interval_sources.andersson: gs://genetics_etl_python_playground/static_assets/andersson2014/enhancer_tss_associations.bed
+step.interval_sources.javierre: gs://genetics_etl_python_playground/static_assets/javierre_2016_preprocessed
+step.interval_sources.jung: gs://genetics_etl_python_playground/static_assets/jung2019_pchic_tableS3.csv
+step.interval_sources.thurman: gs://genetics_etl_python_playground/static_assets/thurman2012/genomewideCorrs_above0.7_promoterPlusMinus500kb_withGeneNames_32celltypeCategories.bed8.gz
step.interval_index_path: '{release_dir}/interval_index'
step.liftover_chain_file_path: 'gs://genetics_etl_python_playground/static_assets/grch37_to_grch38.over.chain'
step.session.write_mode: overwrite

- id: l2g_feature_matrix
prerequisites:
- colocalisation_coloc
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