Immunopipe

Housekeeping and docs updates

- Bump biopipen to 0.18.1
- Mention function changes with versions in docs
- Add apptainer in board.toml so the command can be generated in pipen-board
- Make logo shorter in docs
- Add docker image with `-full` tags to include all dependencies
- Print command help message if run test failed in CI
- Add singularity/apptainer in FAQ for "no space left" question
- Add -w fro apptainer in docs (as we need to save pipen-board file in home directory)

Added

- Add `TESSA` process for [tessa analysis](https://pwwang.github.io/immunopipe/processes/TESSA/)
- Add volcano plot for `MarkersFinder` and `ClusterMarkers`

Fixed

- Fix when `Sample` is the only column in meta for `ImmunarchLoading`
- Add clear message when `k.weight` is too large for `IntegrateData` in `SeuratClustering`
- Allow `unique:` prefix for `on` in `SampleInfo`
- Fix sample order in plots for `SampleInfo`
- Remove `tidyseurat::` prefix for `filter` in scripts of `MetaMarkers`, `ScFGSEA` and `SeuratClusterStats` in case `tidyseurat::filter` is not exported when installed from `conda` (but it will make `dplyr::filter` work anyway on seurat object)

Breaking changes

- Redesign envs for `SeuratClusteringStats` to allow setting defaults for cases and switch identities for plots

Housekeeping and docs updates

- Fix typos in docs/configurations
- `TCRClustering` should be `TCRClusteringStats` in Multi-case variable design section
- `infile` of `[SampleInfo.in]` should be `samples.txt` rather than `sample.txt`
- Remove unused scripts by deprecated processes
- Bump `pipen-report` to [0.12.8](https://github.com/pwwang/pipen-report/releases/tag/0.12.8)
- Add `master` branch and `master` tag as stable tag for docker image
- Add pdf version of the flowchart (4)
- Add warning for the results in getting started tutorial
- Bump `pipen-board` to [0.11.5](https://github.com/pwwang/pipen-board/releases/tag/0.11.5)
- Add apptainer to the docs

Added

- Add `ModuleScoreCalculator` to calculate module scores or cell cycle scores
- See: <https://pwwang.github.io/immunopipe/processes/ModuleScoreCalculator/>
- Allow `SampleInfo` to perform statistics on the sample information
- See: <https://pwwang.github.io/immunopipe/processes/SampleInfo/>
- Add `TCR_Cluster_Size` and `TCR_Cluster_Size1` from `TCRClustering` to metadata for further integrative analysis
- See: <https://pwwang.github.io/immunopipe/processes/TCRClusters2Seurat/>

Fixed

- Fix default height and width for plots in `SeuratClusterStats`
- Fix cluster order not kept after annotation using `hitype` in `CellTypeAnnotation`

Breaking changes

- Change `seurat_clusters_old` to `seurat_clusters_id` to save old `seurat_clusters` in `CellTypeAnnotation`
- Remove `MarkersForClustersOfAllCells` and `TopExpressingGenesOfAllCells` processes
- Rename `MarkersForClustersOfTCells` to `ClusterMarkers`
- Rename `TopExpressingGenesOfTCells` to `TopExpressingGenes`
- Rename `envs.exprs` to `envs.features` for `SeuratClusterStats`
- `envs.exprs.genes` is also renamed to `envs.features.features`

- ⬆️ Bump biopipen to 0.16
- 📝 Add documentation
- 💚 Fix docs building in CI
- 📝 Update README with flowchart

- ✨ Add `TopExpressingGenes`
- 🎨 Move `RadarPlots` to `biopipen`
- ⬆️ Bump biopipen to 0.15.2

- ⬆️ Upgrade biopipen to 0.15.0
- 💚 Use better strategy docker image building

- ⬆️ Bump biopipen to 0.6
- ⬆️ Upgrade other dependencies
- 💚 Use micromamba for docker image building
- ⬆️ Add procps-ng for vdjtools for docker building