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‎.github/workflows/docs.yaml

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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: 3.10.8
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- name: Install and configure Poetry

‎.github/workflows/pytest.yaml

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with:
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fetch-depth: 1
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: 3.10.8
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- name: Install and configure Poetry

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, religion, or sexual identity
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and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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- Demonstrating empathy and kindness toward other people
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- Being respectful of differing opinions, viewpoints, and experiences
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- Giving and gracefully accepting constructive feedback
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- Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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- Focusing on what is best not just for us as individuals, but for the
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overall community
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Examples of unacceptable behavior include:
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- The use of sexualized language or imagery, and sexual attention or
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advances of any kind
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- Trolling, insulting or derogatory comments, and personal or political attacks
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- Public or private harassment
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- Publishing others' private information, such as a physical or email
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address, without their explicit permission
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- Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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.
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series
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of actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or
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permanent ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within
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the community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.0, available at
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https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
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Community Impact Guidelines were inspired by [Mozilla's code of conduct
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enforcement ladder](https://github.com/mozilla/diversity).
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see the FAQ at
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https://www.contributor-covenant.org/faq. Translations are available at
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https://www.contributor-covenant.org/translations.

‎config/datasets/gcp.yaml

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gene_index: ${datasets.outputs}/gene_index
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variant_annotation: ${datasets.outputs}/variant_annotation
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variant_index: ${datasets.outputs}/variant_index
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study_index: ${datasets.outputs}/study_index
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study_locus: ${datasets.outputs}/study_locus
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credible_set: ${datasets.outputs}/credible_set
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summary_statistics: ${datasets.outputs}/summary_statistics
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study_locus_overlap: ${datasets.outputs}/study_locus_overlap
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colocalisation: ${datasets.outputs}/colocalisation
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v2g: ${datasets.outputs}/v2g
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ld_index: ${datasets.outputs}/ld_index
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catalog_study_index: ${datasets.outputs}/catalog_study_index
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catalog_study_index: ${datasets.study_index}/catalog
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catalog_study_locus: ${datasets.study_locus}/catalog_study_locus
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finngen_study_index: ${datasets.outputs}/finngen_study_index
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finngen_summary_stats: ${datasets.outputs}/finngen_summary_stats
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finngen_study_index: ${datasets.study_index}/finngen
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finngen_summary_stats: ${datasets.summary_statistics}/finngen
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from_sumstats_study_locus: ${datasets.study_locus}/from_sumstats
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from_sumstats_pics: ${datasets.credible_set}/from_sumstats
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ukbiobank_study_index: ${datasets.outputs}/ukbiobank_study_index
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ukbiobank_study_index: ${datasets.study_index}/ukbiobank
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l2g_model: ${datasets.outputs}/l2g_model
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l2g_predictions: ${datasets.outputs}/l2g_predictions
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eqtl_catalogue_study_index_out: ${datasets.outputs}/preprocess/eqtl_catalogue/study_index
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eqtl_catalogue_summary_stats_out: ${datasets.outputs}/preprocess/eqtl_catalogue/summary_stats
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# Constants
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finngen_release_prefix: FINNGEN_R9
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finngen_sumstat_url_prefix: gs://finngen-public-data-r9/summary_stats/finngen_R9_
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finngen_sumstat_url_suffix: .gz

‎config/step/finngen.yaml

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_target_: otg.finngen.FinnGenStep
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finngen_phenotype_table_url: ${datasets.finngen_phenotype_table_url}
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finngen_release_prefix: ${datasets.finngen_release_prefix}
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finngen_sumstat_url_prefix: ${datasets.finngen_sumstat_url_prefix}
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finngen_sumstat_url_suffix: ${datasets.finngen_sumstat_url_suffix}
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finngen_study_index_out: ${datasets.finngen_study_index}
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finngen_summary_stats_out: ${datasets.finngen_summary_stats}

‎config/step/gwas_catalog.yaml renamed to ‎config/step/gwas_catalog_ingestion.yaml

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catalog_associations_file: ${datasets.catalog_associations}
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catalog_sumstats_lut: ${datasets.catalog_sumstats_lut}
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variant_annotation_path: ${datasets.variant_annotation}
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ld_index_path: ${datasets.ld_index}
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catalog_studies_out: ${datasets.catalog_study_index}
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catalog_associations_out: ${datasets.catalog_study_locus}

‎config/step/locus_to_gene.yaml

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credible_set_path: ${datasets.credible_set}
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variant_gene_path: ${datasets.v2g}
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colocalisation_path: ${datasets.colocalisation}
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study_index_path: ${datasets.catalog_study_index}
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study_index_path: ${datasets.study_index}
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study_locus_overlap_path: ${datasets.study_locus_overlap}
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gold_standard_curation_path: ${datasets.l2g_gold_standard_curation}
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gene_interactions_path: ${datasets.gene_interactions}

‎config/step/pics.yaml

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_target_: otg.pics.PICSStep
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study_locus_ld_annotated_in: ${datasets.from_sumstats_study_locus}
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picsed_study_locus_out: ${datasets.from_sumstats_pics}
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study_locus_ld_annotated_in: ???
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picsed_study_locus_out: ???

‎config/step/study_locus_overlap.yaml

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_target_: otg.overlaps.OverlapsIndexStep
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study_locus_path: ${datasets.outputs}/catalog_study_locus
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study_index_path: ${datasets.outputs}/catalog_study_index
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study_locus_path: ${datasets.outputs}/credible_set
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study_index_path: ${datasets.outputs}/study_index
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overlaps_index_out: ${datasets.outputs}/study_locus_overlap

‎config/step/variant_index.yaml

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_target_: otg.variant_index.VariantIndexStep
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variant_annotation_path: ${datasets.variant_annotation}
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study_locus_path: ${datasets.study_locus}
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credible_set_path: ${datasets.study_locus}
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variant_index_path: ${datasets.variant_index}

‎docs/python_api/datasource/gwas_catalog/associations.md

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title: Associations
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---
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::: otg.datasource.gwas_catalog.associations.GWASCatalogAssociations
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::: otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser
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---
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::: otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog

‎docs/python_api/datasource/gwas_catalog/study_index.md

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title: Study Index
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---
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::: otg.datasource.gwas_catalog.study_index.GWASCatalogStudyIndex
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::: otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser
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---
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::: otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog

‎docs/python_api/step/gwas_catalog.md

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‎docs/python_api/step/gwas_catalog_ingestion.md

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---
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title: GWAS Catalog
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---
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::: otg.gwas_catalog_ingestion.GWASCatalogIngestionStep

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