.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
*.RData
!globalSetup.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/

.Rproj.user
*.Rproj
.Rhistory
.RData
.Rapp.history
*.RData

.DS_Store

## Added by TMB
# Big data
data/*/*
!data/metadata
!data/demo

READMEbackup.md
!README.md

img/*/*
!img/imapWorkflow*
figures
*.qza

reports/*.html
*.html
*.pptx
*.tmp
*.map
code/Rmd/*.png
code/Rmd/*.pdf
code/Rmd/*.html

results/*/*

resources/refDBs.zip
!resources/progressReports/*.html

*.qsub*
mothur*logfile
*temp*
bbmap
code/mothur
code/FastQC
code/Rmd/report*.html
code/Rmd/global*.html
code/Rmd/figures/*.png
code/bbmap/*
!code/bbmap/bbduk.sh
code/seqkit
code/*win*
code/summarizeFastQC
!code/progressreport*.bash
.CaseStudy/*/*
code/Rmd/*Casestudy.Rmd
# Hidden files
.~*
._*
*.swp

.dockerignore
docker-*.yml
!.git*