.gitignore

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# User-specific files
.Ruserdata

# Genomic Sequences
*.fastq.gz
*.fastq

# 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

# Including the logs folder without content
logs/*
!logs/.gitkeep

# Including the sequences folder without content
sequences/*
!sequences/.gitkeep

# Including the output folder without content
output/*
!output/.gitkeep

# Excluding VSCode settings
.settings.json

# Content of Slurm output folder
slurm/czid/*
slurm/nf-core-mag/*

# Including the Slurm output folder
!slurm/czid/.gitkeep
!slurm/nf-core-mag/.gitkeep

# Content of FastQC output folder
fastqc_analyses/raw_sequences/*
fastqc_analyses/raw_sequences_compressed/
!fastqc_analyses/raw_sequences_compressed/.gitkeep

#MacOS files
.DS_Store

# nf-core results
nf-core-mag/results