.gitignore

# Ignore general files and directories
.Rhistory
.RData
.Ruserdata
.Rproj
.Rproj.user
.DS_Store
scrnaseq2.Rproj
/.quarto/
/book*/
/*_freeze/
/site_libs/

# Ignore files and directories produced in datasets directories (except download.R files and pbmc_datasets.xlsx)
/datasets/**
/test_datasets
!/datasets/**/download.R
!/datasets/pbmc_datasets.xlsx
!/datasets/pbmc_atac.xlsx
!/datasets/10x_visium_human_brain_cancer.xlsx
!/datasets/10x_xenium_mouse_brain.xlsx
!/datasets/10x_SmartSeq2_pbmc_datasets.xlsx
!/datasets/10x_1M_neurons.xlsx

# Ignore files and directories produced in workflow directories (except qmd files)
# To add new modules, comment these lines, create directory and quarto file
# Then run 'git add' and uncomment these lines again
/modules/**
/modules/*/
!/modules/**/*.qmd

# Ignore files and directories produced in docs directory (except qmd files)
/docs/**
/docs/*/
!/docs/*.qmd
!/docs/*.html
!/docs/*.png

# Ignore files and directories produced at the project level
/*.html
/*.md
/*_files


# Ignore quarto local files that should not be cached
environment.local

# Ignore rstudio-server directories
rstudio-server/**