.gitignore

# Personnal notes
/**/notes.txt
/**/*temp*
/**/*tmp*
/**/*.md


# Downloaded data
/**/*.fastq

# Temporary Nextflow files
Nextflow/Temp
Nextflow/work
Nextflow/.*

## New ignores
# ignore temp nextflow files
/**/.nextflow*
# ignore data files
/**/*.csv
/**/*.fa
/**/*.gtf
/**/work
genomeDir
/**/data
/**/alignments
small_test_files
# dotfiles (used to create the workflow dag)
/**/*.dot

# vim
.*.swp
# macOS
.DS_Store

# drafts
truc_ultime.bash

# reference (cheatsheets)
md_ref.md

################### R ignores ####################### 
.Rproj.user

# intermediary reports
src/*.pdf
src/*.tex
src/*.log
src/*.html

# 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/

# 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

####################### Python Ignores

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover

## gh-pages
/**/??*.Rmd
DESCRIPTION
Data/
Dockerfile
Nextflow/
_book/
_bookdown.yml
_bookdown_files/
_build.sh
_deploy.sh
_output.yml
_publish.R
book.bib
bookdown-demo.Rproj
build-site.r
docs/
index.Rmd
licenses/
manual_logs/
now.json
packages.bib
preamble.tex
renv.lock
renv/
site/RNA-seq-CATS-small.png
site/aber.png
site/aquisihay.png
site/assets/
site/baseplot.png
site/bio-TAGI.png
site/data_Nestorowa.csv
site/ggplot2.png
site/hola.png
site/logo.png
site/logo2.png
site/rostizado.png
site/smol-rna.png
site/src/
site/test.png
style.css
test.txt
toc.css