Notable changes:
- Many shell scripts have permission updates to 755 for consistency with other scripts in the repository
- Capture kit definition updates for coyote, phoenix, and tempe
- SigProfiler script updates to only run mutational matrix generation and extraction (useful for genomes that are not supported in cosmic)
- Resource usage reporting scripts are now more dynamic and a bit smarter
- Automatically grouping tasks based on task tags
- Launcher script checks to make sure that the python version used has jetstream installed
- Tempe has updated bwa index generation scripts to make sure that the generated index is alt-aware
- Tempe script usage order in README has been updated to reflect path changes
Expected to support the following pipelines (likely supports lower versions as well):
- Tempe >=v1.2.0
- Phoenix v1.2.0
- Suncity v1.2.1
- Coyote v1.2.1
- Private repositories until extensively tested in a production capacity
- Sonoran v1.2.1
- Bastien v1.2.2
- Monte v1.2.2