Immunopipe

- deps: Bump biopipen to 0.20.7
- deps: Bump pipen-board to 0.13.4
- ClusterMarkers/ClusterMarkersOfAllCells: Choose avg_log2FC > 0 markers by default
- MarkersFinder: Allow to set assay and set assay to `RNA` by default
- CellsDistribution: Add venn/upset plot for overlapping cell groups in different cases
- SampleInfo: Add `distinct` to case to perform stats on distinct records

- ➕ Add `r-ggnewscale` as dependency for `CDR3AAPhyschem` in docker image
- ⬆️ Bump biopipen to 0.20.5
- 🧱 CloneResidency: Integrate RNA data to allow more flexible analysis (i.e. within specific seurat clusters)
- 🏗️ CloneResidency: Rename envs.sample_groups to envs.section to be consistent with other processes
- 📝 ScFGSEA: Remove the link in the summary of the docstring (since they are not transformed in the report)
- 🎨 CDR3AAPhyschem: Give better error message when wrong group items are given
- ⬆️ Bump pipen-board to 0.13.3
- Add items automatically when blurred for list options
- Add other sections to description on the UI for processes

- 🐛 Fix docstring for `RadarPlots`
- ➕ Add `pipen-diagram` as dependency
- ➕ Set `pipen-runinfo` as optional
- ⬆️ Bump biopipen to 0.20.4
- 📝 Update version in docs

Housekeeping and docs

- Bump biopipen to 0.20.3 (pipen to 0.12)
- Use [`pipen-cli-ref`](https://github.com/pwwang/pipen-cli-ref) to generate API for processes (it uses docstring of the process class so that we don't need to maintain two copies of docs)

Fixed/Enhanced

- Make `/data` directory in container, so it can be mounted
- Fix a bug when a single gene provided to `indicator_genes` in `TCellSelection`
- Move `ModuleScoreCalculator` before clustering so that the scores can be used in `vars.to.regress` of `SCTransform` while clustering
- Set default assay to RNA in case module scores only caculated using integrated features in `ModuleScoreCalculator`
- Improve QC plots in `SeuratPreparing` by marking the cells that are removed in the plots instead of doing before/after plots
- Fix type annotation for envs.features_defaults.ncol in docstring for `SeuratPreparing` (causing `pipen-board` not converting to int)
- Fix the cluster order in pie charts for `CellsDistribution`
- Fix the cluster order in pie charts for `SeuratClusterStats`
- Fix order in pie charts for `SampleInfo`
- Fix docstring for `envs.div.args` of `Immunarch` (more clear description of method)
- Allow mutiple columns in the file for `envs.features_defaults.features` in `SeuratClusterStats`
- Allow order to be optional for `CloneResidency` (errored when not provided)
- Add number of clusters at the end of log for `SeuratClusteringOfAllCells`/`SeuratClusteringOfTCells`
- Add stricter checker for input file (13)
- Indicate the case name in logs when pie is enabled for `group-by` in `SeuratClusterStats`
- Allow to skip overlap and gene usage analyses by setting method to `none` for `Immunoarch` (11, 12)
- Don't cluster on heatmap when there are only 2 samples for `TCRClusterStats` (11)
- Import Seurat explictly to avoid satijalab/seurat2853 in `MetabolicFeatures`
- Fix when NA values in data for heatmap in `MetabolicPathwayActivity`
- Fix error when no significant pathways selected in `MetabolicPathwayHeterogeneity`
- Give better error message in CellsDistribution if group value not found for `CellsDistribution` (16)
- Try including more genes (even though insignificant) in volcano plot for `MarkersFinder`/`ClusterMarkers`/`ClusterMarkersOfAllCells` (17)
- Add margins to volcano plot for `MarkersFinder`/`ClusterMarkers`/`ClusterMarkersOfAllCells`
- Fix when `envs.cell_qc` is `None` (not provided) for `SeuratPreparing`
- Fix `ident` in cases of `envs.dimplots` not working for `SeuratClusterStats`

Added

- Add `ClusterMarkersOfAllCells` and `TopExpressingGenesOfAllCells` and set them as optional
- Add dim plots in `SeuratClusterStats` to overlay TCR presence/absence of cells (14)

Breaking changes

- Rename `TCRClusteringStats` to `TCRClusterStats` (15)

- 📝 Fix typos in docs
- 📝 Add links to some optional input files (9, 5)
- 🔨 Add apptainer to docker entry.sh (9, 6)
- 💄 Adjust process order in reports (9, 1)
- ⬆️ Bump pipen-report to 0.13.1 (9, 2)

- Bump biopipen to 0.18.3 to fix when either ident is empty for `MarkersFinder`