.gitignore

# C++
*.o
*.out
*.obj
*.suo
*.user
*.userosscache
*.sln.docstates
*.sdf
*.opensdf
*.vcxproj
*.VC.db
*.VC.VC.opendb
*.idb
*.pdb
*.ilk
*.exe
*.dll
*.lib
*.exp
*.app
*.ipch
*.filters
Debug/
Release/
x64/
x86/
build/
.vs/
*.swp
*.bak
*~
*.vcxproj.filters

# Python
__pycache__/
*.pyc
*.pyo
*.pyd
*.pyc
*.so
*.egg
*.egg-info/
dist/
build/
*.egg-info/
*.eggs/
*.venv/
*.log
*.csv
*.dat
*.out
*.pid
*.gz

# Jupyter Notebook
.ipynb_checkpoints

# IDEs and Editors
.vscode/
.idea/
*.swp
*.swo
*.swn
*.suo
*.bak
*.acm
*.ncb
*.plg
*.bsc
*.ilk
*.exp
*.sbr
*.opt
*.pdb
*.idb
*.pch

# OS generated files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

.idea/**
.gradle
.*.log*
.cache/*
.vagrant/*
.cache/*
.nextflow*
.node-nextflow*
.devcontainer
.vscode/*
*/*/bin/*
**/build/**
build/**
modules/**/build/
modules/**/*.iml
modules/nextflow/work/
**/out/*
tmp/*
work/*
nextflow.eml
nextflow.iml
Vagrantfile
resources/*
test/*
tools/*
tests_other
other
docs/_build/
./*.txt
errors/
misc/
cloud/my-*
docker-test
docker/dist
docker/nextflow
temp
.dockerignore
.launch.classpath
plugins-prod
sandbox
wave-tests

dependencies/*
dependencies/**/*

## Core latex/pdflatex auxiliary files:
*.aux
*.lof
*.log
*.lot
*.fls
*.out
*.toc
*.fmt
*.fot
*.cb
*.cb2
.*.lb

## Intermediate documents:
*.dvi
*.xdv
*-converted-to.*
# these rules might exclude image files for figures etc.
# *.ps
# *.eps
# *.pdf

## Generated if empty string is given at "Please type another file name for output:"
.pdf

## Bibliography auxiliary files (bibtex/biblatex/biber):
*.bbl
*.bcf
*.blg
*-blx.aux
*-blx.bib
*.run.xml

## Build tool auxiliary files:
*.fdb_latexmk
*.synctex
*.synctex(busy)
*.synctex.gz
*.synctex.gz(busy)
*.pdfsync

## Build tool directories for auxiliary files
# latexrun
latex.out/

## Auxiliary and intermediate files from other packages:
# algorithms
*.alg
*.loa

# achemso
acs-*.bib

# amsthm
*.thm

# beamer
*.nav
*.pre
*.snm
*.vrb

# changes
*.soc

# comment
*.cut

# cprotect
*.cpt

# elsarticle (documentclass of Elsevier journals)
*.spl

# endnotes
*.ent

# fixme
*.lox

# feynmf/feynmp
*.mf
*.mp
*.t[1-9]
*.t[1-9][0-9]
*.tfm

#(r)(e)ledmac/(r)(e)ledpar
*.end
*.?end
*.[1-9]
*.[1-9][0-9]
*.[1-9][0-9][0-9]
*.[1-9]R
*.[1-9][0-9]R
*.[1-9][0-9][0-9]R
*.eledsec[1-9]
*.eledsec[1-9]R
*.eledsec[1-9][0-9]
*.eledsec[1-9][0-9]R
*.eledsec[1-9][0-9][0-9]
*.eledsec[1-9][0-9][0-9]R

# glossaries
*.acn
*.acr
*.glg
*.glo
*.gls
*.glsdefs
*.lzo
*.lzs
*.slg
*.slo
*.sls

# uncomment this for glossaries-extra (will ignore makeindex's style files!)
# *.ist

# gnuplot
*.gnuplot
*.table

# gnuplottex
*-gnuplottex-*

# gregoriotex
*.gaux
*.glog
*.gtex

# htlatex
*.4ct
*.4tc
*.idv
*.lg
*.trc
*.xref

# hyperref
*.brf

# knitr
*-concordance.tex
# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
# *.tikz
*-tikzDictionary

# listings
*.lol

# luatexja-ruby
*.ltjruby

# makeidx
*.idx
*.ilg
*.ind

# minitoc
*.maf
*.mlf
*.mlt
*.mtc[0-9]*
*.slf[0-9]*
*.slt[0-9]*
*.stc[0-9]*

# minted
_minted*
*.pyg

# morewrites
*.mw

# newpax
*.newpax

# nomencl
*.nlg
*.nlo
*.nls

# pax
*.pax

# pdfpcnotes
*.pdfpc

# sagetex
*.sagetex.sage
*.sagetex.py
*.sagetex.scmd

# scrwfile
*.wrt

# svg
svg-inkscape/

# sympy
*.sout
*.sympy
sympy-plots-for-*.tex/

# pdfcomment
*.upa
*.upb

# pythontex
*.pytxcode
pythontex-files-*/

# tcolorbox
*.listing

# thmtools
*.loe

# TikZ & PGF
*.dpth
*.md5
*.auxlock

# titletoc
*.ptc

# todonotes
*.tdo

# vhistory
*.hst
*.ver

# easy-todo
*.lod

# xcolor
*.xcp

# xmpincl
*.xmpi

# xindy
*.xdy

# xypic precompiled matrices and outlines
*.xyc
*.xyd

# endfloat
*.ttt
*.fff

# Latexian
TSWLatexianTemp*

## Editors:
# WinEdt
*.bak
*.sav

# Texpad
.texpadtmp

# LyX
*.lyx~

# Kile
*.backup

# gummi
.*.swp

# KBibTeX
*~[0-9]*

# TeXnicCenter
*.tps

# auto folder when using emacs and auctex
./auto/*
*.el

# expex forward references with \gathertags
*-tags.tex

# standalone packages
*.sta

# Makeindex log files
*.lpz

# xwatermark package
*.xwm

# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
# Uncomment the next line to have this generated file ignored.
#*Notes.bib