DEV - Start pipelines #4227
Draft
DEV - Start pipelines #4227
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
add first structure in services
…#4231) (patch) ### Added - Seqera platform submitter - Seqera platform client
### Added - SeqeraPlatformConfig - Method bodies in the SeqeraPlatformClient
## Description ### Added - Abstract Configurator class with abstract method create_config - Base CaseConfig model with attributes `workflow` and `case_id` - RarediseaseConfigurator that creates valid CaseConfig - RarediseaseCaseConfig with attributes `case_priority`, `netxflow_config_file`, `params_file`, and `work_dir` - Fixtures for - RarediseaseCaseConfig - RarediseaseConfigurator - dummy directories - Unit test for Raredisease create_config ### Changed - Separated abstract module into model and service
### Added - DTOs for the Seqera platform endpoints - Tests for the SeqeraPlatformClient
## Description Une one CaseConfig for all nextflow pipelines ### Added - Method `_get_case_workflow` to get the workflow inside the NetflowConfigurator ### Changed - Renamed `RarediseaseCaseConfig` to `NextflowCaseConfig` - Names of fixtures ### Fixed - Removed currently unused elements from config in Configurator
## Description Add infrastructure to build nextflow config files in the RareDisease configurator ### Added - necessary config attributes to build nextflow config to the init of the `RarediseaseConfigurator` - Implemented necessary methods in `RarediseaseConfigurator` - utils module - fixtures - test `for_get_nextflow_config_content` ### Fixed - Removed `__init__` method in abstract class configurator.
2 tasks
## Description ### Fixed - Updates the way of getting the QOS (Slurm priority) whichcasued tests to fail
…(patch) * add code for the params file * add creation of file in create_cpnfig * fix 2 out of 3 failing tests * add also sample sheet code to configurator * fix fixture * add skeleton of new classes * resolve conflicts * stash commit * enhance sample sheet and config * unify classes * stash commit * remove out of scope change * created a nextflow level of inheritance in configurator * add constants for gene files * removed duplicated utils method * renamed write function * rolled back small fix for scope reasons * inject content creators * add gene panel creator * some renaming * add sample sheet creator fixture * add params file creator fixture * add other file creator fixtures * add fixtures in plugins to conftest * fix constructors and fixtures * Add managed_variants support (#4265) (patch) ### Added - ManagedVariantsFileContentCreator * add first tests for content creation * Rework raredisease extension (#4266) * Add managed_variants support * Inject creators * Inject creators * Inject creators * Refactor Raredisease configurator into extension * Fix type hint * Fix fixtures * Fix test * remove inheritance of nextflow configurator (#4267) * remove inheritance of nextflow configurator * add sample sheet path as parameter to params * fix sample sheet path in configurator * address comments * fi sample sheet fixture (#4270) * add todo * fix samplesheet path fixture * Implement Raredisease Extension (#4271) * move raredisease models to the analysis starter directory * rename content creator files * add tests for managed variants * add tests for gene panel * fix sample sheet creator * fix creator * fix sample sheet test * Address comments * Remove TODO * Fix typo * Make interface * Revert interface --------- Co-authored-by: Isak Ohlsson Ångnell <[email protected]> Co-authored-by: islean <[email protected]>
* Initial commit * Change name * Make private * Mark as abstract method * Inject spring archive API * Remove dry run * Remove dry run * (Pipeline Integration) Merge PrepareFastqAPI into the FastqFetcher (#4277) (patch) * Merge PrepareFastqAPI into the FastqFetcher * Add docstrings * Fix sample check * Move to CompressAPI * Return to continue * Address comments * Address comments
### Fixed - Raredisease extension is properly tested
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
Development branch that closes #4031
Added
Changed
Fixed
How to prepare for test
uspaxaHow to test
Expected test outcome
Review
Thanks for filling in who performed the code review and the test!
This version is a
Implementation Plan