Immunopipe

- docs: move `Immunarch` to the later position in process list
- docs: Use `master` tag in getting-started

- chore: change line length to 88 for flake8
- chore: dismissing warning about wasting columns for `SeuratClusteringOfTCells`
- docs: update CHANGELOG.md with missing changes of last version
- docs: add version of renaming `envs.tcell_indicator` to `envs.tcell_selector`
- docs: remove unused doc files
- docs: add metadata illustration
- deps: bump biopipen to 0.22.8. Highlights:
- deps: bump pipen-board to 0.13.10 (pipen-report to 0.16.2)
- CellsDistribution: Don't add rownames to the output table file
- MarkersFinder (ClusterMarkers/ClusterMarkersOfAllCells): Optimize to use `FindAllMarkers` if `ident.1` is not specified
- SeuratClusterStats: Fix path of expression table file
- CellTypeAnnotation: Allow using `NA` to exclude clusters from output `Seurat` object
- utils.mutate_helpers: Return ids only when subset is true and group is not `NA` for `uniq = TRUE` in `expanded`, `collapsed`, `emerged` and `vanished`

- deps: update biopipen to 0.22.1, highlights:
- add V-J junction circos plots to `Immunarch` process
- add cache option to cache the clustering results if nothing changed except ncores, to `SeuratClustering` process
- add dot plots to `MarkersFinder` (`ClusterMarkersOfAllCells`, `ClusterMarkers`) process
- save exported table with only necessary columns for `CellsDistribution` process
- add `descr` to describe cases cases in report for `CellsDistribution` process
- add `subset` for dimplots in `SeuratClusterStats` process
- use a new palette (`biopipen`) for related processes
- optimize report rendering (using `render_job()` filter from `pipen-report`)
- change metacols to extracols so essential columns get exported for `ImmunarchLoading` process
- add cache option to cache the clustering results if nothing changed except ncores for `SeuratClustering` (`SeuratClusteringOfAllCells`) process
- see more at <https://github.com/pwwang/biopipen/releases/tag/0.22.0> and <https://github.com/pwwang/biopipen/releases/tag/0.22.1>
- deps: update pipen-report to 0.16, highlights:
- scroll anchor into view on the page
- build report page when each process is done, instead of the whole pipeline
- see more at <https://github.com/pwwang/pipen-report/releases/tag/0.16.0>
- change: remove `Immunarch2VDJtools` and `VJUsage` processes (vj usage analysis can be done in `Immunarch` process)
- change: change `tcell_indicator` to `tcell_selector` in `TCellSelection` process
- enhance: provide better error message when none barcode matches from RNA and TCR data for `TCRClustering` process
- docs: add memory usage reduction tips in FAQ
- chore: dismiss warnings of wasted input columns for multiple processes

- chore: update pipeline description to include version in the logs
- fix: add fc-cache command to Dockerfile to solve `Fontconfig error`
- docker: optimize building full image based off the base image

- docker: lock r-matrix version to 1.6_1 for compatibility
- docs: adopt mkdocs-rtd 0.0.10 (add scrollbar to the table of contents)
- deps: bump biopipen to 0.21.1
- use `r-logger` for logging in R scripts
- docs: fix internal references in API docs
- deps: bump pipen-board to 0.13.6
- SampleInfo: refactor data subset logic using `subset` instead of `distinct`
- Immunarch: add `in.metafile` to allow other meta info (i.e. seurat clusters) for future subsetting (22)
- Immunarch: fix empty groups in diversity plot after subsetting
- Immunarch: allow `subset` to subset cells for analyses
- Immunarch: allow `separate_by` also works on other diversity plots
- Immunarch: add `ymin` and `ymax` to align diversity plots by `separate_by`
- Immunarch: add `ncol` to specify columns in the combined plots
- RadarPlots: fix `envs.order` not working
- MarkersFinder: add `overlap` to find overlapping markers between cases (24)
- MarkersFinder: allow `subset` to subset cells for analyses
- MarkersFinder: add dot plots for significant markers
- CellsDistribution: allow multiple columns for `cells_by`
- CellsDistribution: allow `subset` to subset cells for analyses
- utils.mutate_helpers.R: add `include_emerged` for `expanded()` and `include_vanished` for `collapsed()`

- 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