chore: format yaml files

.github/workflows/pr.yaml

@@ -1,8 +1,9 @@
+---
 name: Checks
-"on":
+'on':
   pull_request:
 env:
-  PYTHON_VERSION_DEFAULT: "3.10.8"
+  PYTHON_VERSION_DEFAULT: '3.10.8'
 jobs:
   test:
     runs-on: ubuntu-latest

.github/workflows/push_config.yaml

@@ -1,3 +1,4 @@
+---
 # push config file to the google cloud storage
 name: Push Config
 on:

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+---
 default_language_version:
   python: python3.10
 ci:

docker-compose.yaml

@@ -1,3 +1,4 @@
+---
 # Licensed to the Apache Software Foundation (ASF) under one
 # or more contributor license agreements.  See the NOTICE file
 # distributed with this work for additional information

src/ot_orchestration/dags/config/credible_set_qc.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   python_main_module: gs://genetics_etl_python_playground/initialisation/gentropy/dev/cli.py
   cluster_metadata:

src/ot_orchestration/dags/config/eqtl_catalogue_ingestion.yaml

@@ -1,3 +1,4 @@
+---
 eqtl_catalogue_raw_susie_glob: gs://eqtl_catalogue_data/ebi_ftp/susie/**/*.gz
 eqtl_catalogue_decompressed_susie_path: gs://eqtl_catalogue_data/ebi_ftp/susie_decompressed_tmp
 decompression_logs: gs://eqtl_catalogue_data/ebi_ftp/susie_decompressed_tmp/logs.log

src/ot_orchestration/dags/config/finngen_ingestion.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   python_main_module: gs://genetics_etl_python_playground/initialisation/gentropy/dev/cli.py
   cluster_metadata:
@@ -19,7 +20,7 @@ nodes:
       step.finngen_release_prefix: FINNGEN_R11
       step.finngen_summary_stats_url_prefix: gs://finngen-public-data-r11/summary_stats/finngen_R11_
       step.sample_size: 453733
-      step.finngen_summary_stats_url_suffix: ".gz"
+      step.finngen_summary_stats_url_suffix: '.gz'
       step.efo_curation_mapping_url: https://raw.githubusercontent.com/opentargets/curation/24.09.1/mappings/disease/manual_string.tsv
       step.session.write_mode: overwrite
       step.session.start_hail: true

src/ot_orchestration/dags/config/finngen_ukb_meta_harmonisation.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   python_main_module: gs://genetics_etl_python_playground/initialisation/gentropy/szsz-update-package-for-dataproc-run/cli.py
   cluster_metadata:

src/ot_orchestration/dags/config/genetics_etl.yaml

@@ -1,3 +1,4 @@
+---
 l2g_gold_standard_path: gs://genetics_etl_python_playground/input/l2g/gold_standard/curation.json
 release_dir: gs://ot_orchestration/releases/24.10_freeze6
 dataproc:
@@ -11,7 +12,6 @@ dataproc:
   num_workers: 10
 
 nodes:
-
   - id: gene_index
     kind: Task
     prerequisites: []
@@ -127,7 +127,7 @@ nodes:
         boot_disk_mib: 10000
       task_specs:
         max_retry_count: 1
-        max_run_duration: "2h"
+        max_run_duration: '2h'
       policy_specs:
         machine_type: n1-standard-4
     params:
@@ -161,7 +161,7 @@ nodes:
       step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze6/credible_set
       step.coloc_path: gs://ot_orchestration/releases/24.10_freeze6/colocalisation/
       step.colocalisation_method: Coloc
-      +step.colocalisation_method_params: "{priorc1: 1e-4, priorc2: 1e-4, priorc12: 1e-5}"
+      +step.colocalisation_method_params: '{priorc1: 1e-4, priorc2: 1e-4, priorc12: 1e-5}'
 
   - id: l2g_feature_matrix
     prerequisites:
@@ -187,7 +187,7 @@ nodes:
       step.run_mode: train
       step.wandb_run_name: 24.10_freeze6
       step.hf_hub_repo_id: opentargets/locus_to_gene
-      step.hf_model_commit_message: "chore: update model based on 24.10_freeze6 run"
+      step.hf_model_commit_message: 'chore: update model based on 24.10_freeze6 run'
       step.model_path: gs://ot_orchestration/releases/24.10_freeze6/locus_to_gene_model/classifier.skops
       step.credible_set_path: gs://ot_orchestration/releases/24.10_freeze6/credible_set
       step.variant_index_path: gs://ot_orchestration/releases/24.10_freeze6/variant_index

src/ot_orchestration/dags/config/gnomad_ingestion.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   python_main_module: gs://genetics_etl_python_playground/initialisation/gentropy/dev/cli.py
   cluster_metadata:

src/ot_orchestration/dags/config/gwas_catalog_sumstats_pics.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   cluster_name: otg-gwascatalog-sumstats-pics
   autoscaling_policy: otg-preprocess-gwascatalog

src/ot_orchestration/dags/config/gwas_catalog_sumstats_susie_clumping.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   python_main_module: gs://genetics_etl_python_playground/initialisation/gentropy/dev/cli.py
   cluster_metadata:

src/ot_orchestration/dags/config/gwas_catalog_sumstats_susie_finemapping.yaml

@@ -1,3 +1,4 @@
+---
 nodes:
   - id: generate_manifests
     kind: Task
@@ -24,6 +25,6 @@ nodes:
         boot_disk_mib: 20_000
       task_specs:
         max_retry_count: 1
-        max_run_duration: "7200s"
+        max_run_duration: '7200s'
       policy_specs:
         machine_type: n2-highmem-4

src/ot_orchestration/dags/config/gwas_catalog_top_hits.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   cluster_name: otg-tophit-gwascatalog
   autoscaling_policy: otg-gwascatalog-tophit

src/ot_orchestration/dags/config/ukb_ppp_eur_finemapping.yaml

@@ -1,3 +1,4 @@
+---
 nodes:
   - id: generate_manifests
     kind: Task
@@ -24,6 +25,6 @@ nodes:
         boot_disk_mib: 20_000
       task_specs:
         max_retry_count: 5
-        max_run_duration: "7200s"
+        max_run_duration: '7200s'
       policy_specs:
         machine_type: n2-highmem-4

src/ot_orchestration/dags/config/ukb_ppp_eur_harmonisation.yaml

@@ -1,3 +1,4 @@
+---
 dataproc:
   python_main_module: gs://genetics_etl_python_playground/initialisation/gentropy/dev/cli.py
   cluster_metadata: