.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# 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/
*.Rproj

# 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/

# Markdown output
notebooks/downstream_analysis_files
notebooks/downstream_analysis.md

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

# R Environment Variables
.Renviron

# Ignore results folders
*results/

# Ignore temporary folders
_STARtmp/
Log.out

# Ignore cluster files
setup_pipeline.sh.e*
setup_pipeline.sh.o*
parallel_samples.sh.e*
parallel_samples.sh.o*
multiqc.sh.e*
multiqc.sh.o*

# Ignore nextflow outputs
*.nextflow*
work/

# cluster logs
*.sh.e*
*.sh.o*