Immunopipe

- docs: update table in gallery
- deps: use [pipen-poplog](https://github.com/pwwang/pipen-poplog) to populate job logs to pipeline running log
- deps: bump biopipen to 0.24. Hights:
- scrna.ScFGSEA: add subset to filter cells (pwwang/biopipen112) yuey11
- scrna.SeuratClustering/SeuratSubClustering: cache Seurat procedures step by step (40) xyfqwlzoe
- tcr.Immunarch: add `plot_type` to support boxplots for diversity metrics
- see more at <https://github.com/pwwang/biopipen/releases/tag/0.24.0>

- change: do not rescale gene expression in `TCellSelection` any more
- fix: fix column names of indicators not aligned with `indicator_genes`
- feat: add feature plots in `TCellSelection`
- deps: bump biopipen to 0.23.8
- scrna.SeuratPreparing: log Seurat procedure arguments
- scrna.ScFGSEA: add `subset` to filter cells (pwwang/biopipen112)

- deps: bump biopipen to 0.23.7
- scrna.SeuratPreparing: update log message for transformation/scaling step
- scrna_metabolic_landscape.MetabolicPathwayHeterogeneity: add utils.gsea script source to support `localizeGmtfile`

- deps: add r-seuratdisk dependency to conda env files. yuey11
- deps: pin r-matrixstats to 1.1.0 in conda env files to fix `useNames = NA` error. yuey11
- refactor: optimize configuration file validation
- deps: bump biopipen to 0.23.6
- feat: support url for gmtfile wherever GSEA is performed (pwwang/biopipen113)
- tcr.Immunarch: add error message for empty filtered/subset data in diversity
- scrna.SeuratPreparing: correct description of default assay in docstr
- scrna.SeuratPreparing: run also the normal normalization procedures when `SCTransform` is used (useful for visualization purposes on RNA assay)
- scrna.ModuleScoreCalculator: document the names added by cell cycle score (34)
- scrna.SeuratPreparing: support sample names as `reference` for `IntegrateLayers`

- deps: add bioconductor-glmgampoi to conda env files (33)
- docs: correct the Seurat object assay description
- deps: bump biopipen to 0.23.5
- fix: fix when no enriched items found for `scrna.MarkersFinder`, `scrna.MetaMarkers` and `scrna.TopExpressingGenes`
- scrna.SeuratClusterStats: fix when `frac` or `frac_ofall` is true and no `group-by` nor `split-by` is specified for `stats`
- utils.gsea.R: fix when no enriched items found for `runEnrichr`
- scrna_metabolic_landscript: fix adding report when `ncores` > 1

- docs: add gallery section to README.md
- change: set default `nstart` of kmeans to 25 in `TCellSelection`
- deps: add `r-hdf5r` in conda env files to support `Read_10x_h5` from Seurat. yuey11
- deps: bump biopipen to 0.23.4
- scrna.TopExpressingGenes: fix colnames while pulling average expression
- scrna.CellsDistribution: fix when `cells_by` has multiple column names
- scrna.CellTypeAnnotation: fix the order of the clusters for `direct` method
- scrna.SeuratClusterStats: add `position` options for bar plots for stats
- scrna.RadarPlots: add `colors` to set the colors of the loops in radar and bar plots
- tcr.Immunarch: add `split_by` and `split_order` to put subplots together in one single plots