.gitignore

# Default ----

# Ok to keep a copy of this, but don't need to 
# record every update
run_slurm.sh

# Internal README
README_internal.md

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# User-specific files
.Ruserdata

# RStudio files
.Rproj.user/
README.html

# R Environment Variables
.Renviron

# Custom for rr ----

# Exclude data
data
*/data
*/*/data

# Exclude logs
logs

# Exclude exploratory
exploratory

# Exclude the CNV analysis
singlecell_tumor/

# Exclude some output
bulk_transcriptome_epigenome/output/01

# Exclude pdfs, which take up more space
figures/*/*.pdf
*/figures/*/*.pdf

# Exclude source data
figures/*/*.source_data.tsv
*/figures/*/*.source_data.tsv

# Exclude .Rda/Rds files
output/*/*.Rda
*/output/*/*.Rda
output/*/*.Rds
*/output/*/*.Rds
.Rproj.user

# Exclude rendered HTML files
*/analysis/*.html