Code

Refactor and add test actions#93

Code

Merged

endast merged 108 commits intomainPMBio/deeprvat:mainfrom feature/more-pipeline-smoketestsPMBio/deeprvat:feature/more-pipeline-smoketestsCopy head branch name to clipboardMay 24, 2024

+292-276

Commits

Commits on May 15, 2024

• Add run_training pipeline

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• Add actual smoke test

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• Update github-actions.yml

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• Update github-actions.yml

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• Split jobs

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• Update github-actions.yml

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• Fix deps in actions

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• Shorter names

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• Make preprocessing paralell

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• New name

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• Test reusable code

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• Update github-actions.yml

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• Update github-actions.yml

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• Update setup-deeprvat-env.yaml

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• Update github-actions.yml

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• test

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• Remove reusable

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Commits on May 16, 2024

• Add reginie

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• Typo

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• Cleanup

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• Fix path to pipeline

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• Remove workflow

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• Create reusable workflow

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• Use relative path

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• Update smoke-tests.yml

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• fix path

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• Update smoke-tests.yml

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• Update smoke-tests.yml

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• Fix type

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• fix path

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• Update smoke-tests.yml

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• With steps

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• add pre run cmd

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• test whole pipeline

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Commits on May 17, 2024

• Merge branch 'main' into feature/more-pipeline-smoketests

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• Update smoke-tests.yml

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• Update smoke-tests.yml

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• update

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• Update smoke-tests.yml

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• Fix path

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• install deeprvat

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• Update smoke-tests.yml

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• Move gpu conf fix

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• Update pipeline-tests.yml

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• add dry run flag

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• update

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• Update run-pipeline.yml

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• Update run-pipeline.yml

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• Update run-pipeline.yml

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• Update run-pipeline.yml

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• Update run-pipeline.yml

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• Update pipeline-tests.yml

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• Update pipeline-tests.yml

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• All Smoke tests added

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• Update pipeline-tests.yml

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• add Pipeline-Tests-Training-Association-Testing

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• Add Pipeline-Tests-Association-Testing-Pretrained-Regenie

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• Add missing tests

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• Update pipeline-tests.yml

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• add annotation smoke

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• Correct pipeline

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• Update run-pipeline.yml

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• Update pipeline-tests.yml

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• Add config

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• Update pipeline-tests.yml

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• Add comments

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• Add download_example_data

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• Add preprocssing pipeline full runs

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• bug fixes for REGENIE pipelines

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• Add preprocessing config and directory

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• Update run-pipeline.yml

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• Update run-pipeline.yml

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• Fix paths

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• retry

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• Update run-pipeline.yml

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• Update pipeline-tests.yml

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• Merge remote-tracking branch 'origin/bug-regenie-pipelines' into feature/more-pipeline-smoketests

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• Only preprocessing

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• Update run-pipeline.yml

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• fixup! Format Python code with psf/black pull_request

  

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• add GTF file

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• Merge branch 'bug-regenie-pipelines' of github.com:PMBio/deeprvat into bug-regenie-pipelines

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• Update run-pipeline.yml

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• Update run-pipeline.yml

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• Use correct env

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• Add annotations pipeline

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• add Seed Gene Discovery

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• Add Association Testing Training

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• add Training Pipeline and pretrained

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• Add regenie pipelines

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• Fix names

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• Merge branch 'bug-regenie-pipelines' into feature/more-pipeline-smoketests

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• Use name from job

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• remove name

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• remove name

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• Refactor

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• update name

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• Revert "Remove workflow"

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• Add pytest runner

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• Fix test path

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• No paralell tests for preprocessing

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Commits on May 21, 2024

• Merge branch 'main' into feature/more-pipeline-smoketests

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• Merge branch 'main' into feature/more-pipeline-smoketests

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Commits on May 22, 2024

• Merge branch 'main' into feature/more-pipeline-smoketests

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Commits on May 23, 2024

• add missing sample file

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• Merge branch 'bug-regenie-pipelines' into feature/more-pipeline-smoketests

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Commits on May 24, 2024

• Merge branch 'main' into feature/more-pipeline-smoketests

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• change to fasta download

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