Rename is_sample_source_type_ffpe #4670
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## Description This PR adds logic to configure a Balsamic case
## Description Add a step of linking FASTQ files into the correct directory. ## Added - linking to the new config_case method for balsamic
## Description Adds the CLI template that BalsamicCaseConfig will be dumped into ### Added - CLI string template for Balsamic run CLI command ### Fixed - Pass kwargs flags to the method using them
## Description Adds a Balsamic tracker specifying where to find the SLURM ids and the Balsamic version ### Added - BalsamicTracker
## Description ### Added - Add support for Balsamic in the StarterFactory
## Description This PR hooks up the new logic to dev-commands ### Added - Balsamic dev-commands
## Description ### Added - Added `cancer-somatic-snv-observations` which was missing ### Changed - Removed `cancer-germline-sv-observations` as balsamic doesn't even accept it - Changed pon fetching to return None instead of raising an error if no file is found ### Fixed - Removed extra "balsamic" in CLI method invocation
### Added - Changes needed for Balsamic v18 - The BalsamicConfigFileCreator. --------- Co-authored-by: Mathias Johansson <[email protected]> Co-authored-by: Rasmus Burge <[email protected]> Co-authored-by: islean <[email protected]> Co-authored-by: Linnéa Löfdahl <[email protected]> Co-authored-by: Isak Ohlsson Ångnell <[email protected]> Co-authored-by: Vincent Janvid <[email protected]>
- Tests for `start_command` in `BalsamicCaseConfig` - BALSAMIC added to parameterized tests for sub processor where `start_command` is called
--------- Co-authored-by: Rasmus Burge <[email protected]> Co-authored-by: Sebastian Diaz <[email protected]> Co-authored-by: islean <[email protected]> Co-authored-by: Isak Ohlsson Ångnell <[email protected]>
Co-authored-by: Sebastian Diaz <[email protected]>
Co-authored-by: Sebastian Diaz <[email protected]>
Co-authored-by: Sebastian Diaz <[email protected]>
…-new-start-balsamic
diitaz93
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Oct 28, 2025
diitaz93
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Oct 28, 2025
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diitaz93
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Shouldn't it be is_sample_source_not_ffpe?
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Description
Renaming of function to match the result of the function.
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