.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# 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

# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
rsconnect/

# Files from unexpected exit
.nfs*

# Snakemake files
.snakemake
.Snakefile.swp
.snakemake/*

# Data that are too big
test/snakejob*
test/demultiplexed_fastq
test/demultiplexed_fastq_gz

#cached python files
scripts/__pycache__/*

config_361.yml
config_499.yml
.DS_Store
test/QIIME_output/
test/cluster_logs/
test/manifest.csv
test/total_read_counts.tsv
test/report.RData