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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 <math.joh.bio@gmail.com> Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com> Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com> Co-authored-by: Vincent Janvid <vincent.janvid@scilifelab.se>
Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se>
Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se>
Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se>
…-new-start-balsamic
* add new balsamic test * parametrise balsamic and mip dna tracker tests * remove original test * fix tests * refactor typedmock import * Update tests/services/analysis_starter/tracker/test_tracker_for_slurm_pipelines.py Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com> * Update tests/services/analysis_starter/tracker/test_tracker_for_slurm_pipelines.py Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com> * rename test file --------- Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com>
## Added - Parameterized the two existing balsamic start-available tests to also run the refactored command and expect the same results - Create (empty) files where the BalsamicAPI will look for them when creating flags for the config case command to make the tests more complete. ## Changed - Updated existing balsamic integration tests to include changes made for Balsamic v.18 - Moved non-fixture functions from contest to a new utils module specific to integration test code - Alphabetically sorted flags sent to the config case command in BalsamicAPI to make it easier to compare them to the refactored counterparts which are also sorted.
* move all loqusdb dumps into the correct group * Fix test and attribute access * Green state with new config structure * GREEN! * rename_variable in config file creator * fix error message --------- Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com>
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