.gitignore

# Data folders and large files 
**/input/
**/output/
**/data/
**/tmp
**/tmp_output
**/results/
**/logs/
**/outs/
**/figures/
**/.ipynb_checkpoints/
**/zenodo_tarfiles/

# Large files 
.csv
.tsv
.pdf
.png
.jpeg
.svg
.tiff

.gz
.tar
.tgz

.RData
.RDS

.fa
.fq
.fasta
.fastq
.bam
.ioe
.gtf

# Object generation 
*_prepare_inputs.ipynb

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData
.RDataTmp
.ipynb_checkpoints/

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# RStudio files
.Rproj.user/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
*_cache/
/cache/

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# R Environment Variables
.Renviron

# pkgdown site
docs/

# translation temp files
po/*~

# RStudio Connect folder
rsconnect/