# Created by https://www.gitignore.io/api/r,perl,linux,macos,python,windows,microsoftoffice # Edit at https://www.gitignore.io/?templates=r,perl,linux,macos,python,windows,microsoftoffice ### 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 ### MicrosoftOffice ### *.tmp # Word temporary ~$*.doc* # Word Auto Backup File Backup of *.doc* # Excel temporary ~$*.xls* # Excel Backup File *.xlk # PowerPoint temporary ~$*.ppt* # Visio autosave temporary files *.~vsd* ### Perl ### !Build/ .last_cover_stats /META.yml /META.json /MYMETA.* *.o *.pm.tdy *.bs # Devel::Cover cover_db/ # Devel::NYTProf nytprof.out # Dizt::Zilla /.build/ # Module::Build _build/ Build Build.bat # Module::Install inc/ # ExtUtils::MakeMaker /blib/ /_eumm/ /*.gz /Makefile /Makefile.old /MANIFEST.bak /pm_to_blib /*.zip ### Python ### # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] *$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. *.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 .hypothesis/ .pytest_cache/ # Translations *.mo *.pot # Scrapy stuff: .scrapy # Sphinx documentation docs/_build/ # PyBuilder target/ # pyenv .python-version # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. # However, in case of collaboration, if having platform-specific dependencies or dependencies # having no cross-platform support, pipenv may install dependencies that don't work, or not # install all needed dependencies. #Pipfile.lock # celery beat schedule file celerybeat-schedule # SageMath parsed files *.sage.py # Spyder project settings .spyderproject .spyproject # Rope project settings .ropeproject # Mr Developer .mr.developer.cfg .project .pydevproject # mkdocs documentation /site # mypy .mypy_cache/ .dmypy.json dmypy.json # Pyre type checker .pyre/ ### R ### # 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.Bookdown Stack ### # R package: bookdown caching files /*_files/ ### Windows ### # Windows thumbnail cache files Thumbs.db Thumbs.db:encryptable 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,linux,macos,python,windows,microsoftoffice # nextflow analysis folders/files /test_data/* !/test_data/createTestData.sh !/test_data/Replicate_For_Input_Bag(test).json /workflow/.nextflow/* /workflow/work/* /workflow/output/* /.nextflow/* /data/* /work/* /output/* pipeline_trace*.txt* .nextflow*.log* report*.html* timeline*.html* *~ *.tmp *.swp *.out *_studyRID.json *_studyRID.csv run*.sh !.gitkeep