(Pipeline implementation) Implement seqera submitter #4243
Conversation
…ubmitter # Conflicts: # tests/conftest.py
cg/services/analysis_starter/configurator/models/raredisease.py
Outdated
Show resolved
Hide resolved
| parameters: dict = ReadFile.get_content_from_file( | ||
| file_format=FileFormat.YAML, file_path=case_config.params_file | ||
| ) | ||
| parameters_as_string = WriteStream.write_stream_from_content( | ||
| content=parameters, file_format=FileFormat.YAML | ||
| ) |
There was a problem hiding this comment.
This is a bit ugly - happy to take suggestions if there are easier ways to read the file contents into a yaml formatted string
There was a problem hiding this comment.
you could create a function in the ReadFile module get_stream_from_file that does this
cg/services/analysis_starter/submitters/seqera_platform/submitter.py
Outdated
Show resolved
Hide resolved
cg/services/analysis_starter/configurator/implementations/raredisease.py
Outdated
Show resolved
Hide resolved
…ubmitter # Conflicts: # cg/services/analysis_starter/configurator/implementations/raredisease.py
…ubmitter # Conflicts: # cg/services/analysis_starter/configurator/implementations/raredisease.py # cg/services/analysis_starter/configurator/models/nextflow.py # tests/conftest.py # tests/fixture_plugins/analysis_starter/case_config_fixtures.py # tests/fixture_plugins/analysis_starter/path_fixtures.py
| def raredisease_repository() -> str: | ||
| return "http://some_url" | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def raredisease_revision() -> str: | ||
| return "2.2.0" | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def raredisease_config_profiles() -> list[str]: | ||
| return ["myprofile"] |
There was a problem hiding this comment.
These have to match the parameters in the context_config fixture. Would it use these there instead? Or should these fixtures take the context_config as input?
| params_file=raredisease_params_file_path.as_posix(), | ||
| pipeline_repository=raredisease_repository, | ||
| pre_run_script="", |
There was a problem hiding this comment.
For now, no data here. Maybe we should populate it but seems a bit early to go into such detail?
|
Description
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