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Flexible pseudobulk designs, robust annotations and improved visualization - #15
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…re_input for x5k and ate; backs up the user's metadata and reformats to the required 2-column shape)
…ata normaliser per sample
fix: external metadata loading and geojson tracking
- Define base_path in config.yaml - Incldue base_path in config.schema.yaml - Define all project paths relative to base_path - Include instructions on how to correctly define such paths - Add function to parse all config variables and expand base_path - Include common.smk before config loading and processing - Validate config schema after expanding base_path
- Updated .test config.yaml to include base_dir variable - Set directory: .test under the default profile Default workflow now runs under .test directory
- replace machine-specific paths with configurable placeholders - document profile working-directory requirements - fix Xenium output path handling - set default gene query and cell marker files
Fix linting bug by improving pipeline configuration with several commits that: - Define configuration paths as relative to `base_dir` variable or as placeholders that must be modified. - Use `.test/` directory as the target of the default profile - Add graphviz as a dependency of the development environment - Minor corrections
…ly available cell annotations
The four-PR stack is ready to merge in order: #9 → #11 → #12 → #13. The branches have been rebased so that each PR is based directly on the preceding one. Conflicts between the metadata fixes, annotation-selection behavior, and plotting changes were resolved while preserving read-only metadata handling and the AnnData annotation fallback. The full stack passes formatting, linting, and the 25-job Snakemake dry-run.
…params and files in config
…eated unpaired DE designs
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What & why
Merge new extended capabilities from
devbranch for v0.5.0 release.Validation
.test/.test/dry-run builds the CoreBlock DAGworkflow/schemas/config.schema.yamlmkdocs build --strictpasses, if documentation was changed.smkrules and scripts; documentation was updated if behaviour changed