Update gitignore

.gitignore

@@ -24,6 +24,120 @@ wheels/
 .installed.cfg
 *.egg
 
+# PyInstaller
+# Created by https://www.gitignore.io/api/r,perl,macos,linux,python,windows
+# Edit at https://www.gitignore.io/?templates=r,perl,macos,linux,python,windows
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Perl ###
+!Build/
+.last_cover_stats
+/META.yml
+/META.json
+/MYMETA.*
+*.o
+*.pm.tdy
+*.bs
+
+# Devel::Cover
+cover_db/
+
+# Devel::NYTProf
+nytprof.out
+
+# Dizt::Zilla
+/.build/
+
+# Module::Build
+_build/
+Build
+Build.bat
+
+# Module::Install
+inc/
+
+# ExtUtils::MakeMaker
+/blib/
+/_eumm/
+/*.gz
+/Makefile
+/Makefile.old
+/MANIFEST.bak
+/pm_to_blib
+/*.zip
+
+### Python ###
+# 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.
@@ -37,6 +151,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
@@ -44,6 +159,7 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -52,6 +168,7 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
+db.sqlite3
 
 # Flask stuff:
 instance/
@@ -69,6 +186,10 @@ target/
 # Jupyter Notebook
 .ipynb_checkpoints
 
+# IPython
+profile_default/
+ipython_config.py
+
 # pyenv
 .python-version
 
@@ -84,6 +205,8 @@ celerybeat-schedule
 env/
 venv/
 ENV/
+env.bak/
+venv.bak/
 
 # Spyder project settings
 .spyderproject
@@ -97,10 +220,83 @@ ENV/
 
 # mypy
 .mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### Python Patch ###
+.venv/
+
+### R ###
+# 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
+
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.gitignore.io/api/r,perl,macos,linux,python,windows
 
 # nextflow analysis folders/files
-/test_data/*.fastq.gz
-/test_data/*.fastq
+/test_data/*
 /workflow/.nextflow/*
 /workflow/work/*
 /workflow/output/*
@@ -110,3 +306,5 @@ report.html*
 timeline*.html*
 
 *~
+
+!.gitkeep

test_data/design.csv

-Sample,fastq_R1,fastq_R2
-D17PrPzF_BE,D17PrPzF_BE_S1_L001_R1_001.fastq.gz,D17PrPzF_BE_S1_L001_R2_001.fastq.gz
-D17PrPzF_BE,D17PrPzF_BE_S1_L002_R1_001.fastq.gz,D17PrPzF_BE_S1_L002_R2_001.fastq.gz
-D17PrPzF_LE,D17PrPzF_LE_S3_L001_R1_001.fastq.gz,D17PrPzF_LE_S3_L001_R2_001.fastq.gz