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.gitignore
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.gitignore
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# Logs
logs
*.log*
# Runtime data
pids
*.pid
*.seed
# Directory for instrumented libs generated by jscoverage/JSCover
lib-cov
# Coverage directory used by tools like istanbul
coverage
# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
.grunt
# node-waf configuration
.lock-wscript
# Compiled binary addons (http://nodejs.org/api/addons.html)
build/Release
# Dependency directory
# https://www.npmjs.org/doc/misc/npm-faq.html#should-i-check-my-node_modules-folder-into-git
node_modules
#dist folder
dist
# IDEA/Webstorm project files
.idea
*.iml
#VSCode metadata
.vscode
# Mac files
.DS_Store
# R files
.Rproj.user
.Rhistory
.RData
.Ruserdata
# VSCode
*.code-workspace
# Python files
python/__pycache__/**/*
# Created by https://www.gitignore.io/api/jupyternotebooks
# Edit at https://www.gitignore.io/?templates=jupyternotebooks
### JupyterNotebooks ###
# gitignore template for Jupyter Notebooks
# website: http://jupyter.org/
.ipynb_checkpoints
*/.ipynb_checkpoints/*
# IPython
profile_default/
ipython_config.py
# Remove previous ipynb_checkpoints
# git rm -r .ipynb_checkpoints/
# End of https://www.gitignore.io/api/jupyternotebooks
# Ignore PDBs
pymol/pdbs/**/*
# Ignore all notebooks
notebooks/**
# Old versions
versions/**
# Server pycache
server/decrypt_function/__pycache__/**
# Snakemake files
example_data/**
.snakemake/**
workflow*/.snakemake/**
workflow*/**/__pycache__/**
**/__pycache__/**
# Ignore data folder/links
data/**
data_genbank/**
data_custom/**
data_flu/**
data_gisaid_flu/**
data_gisaid_rsv/**
data_genbank_rsv/**
data_6month
data_6month/**
# Ignore server passwords
server/htpasswd
# Ignore site deployment scripts
push_data.sh
daily_update.sh
daily_update_new.sh
daily_update_rsv.sh
daily_update_sars2_genbank.sh
daily_update_sars2_gisaid_full.sh
daily_update_sars2_gisaid_6month.sh
update_gisaid.sh
update_genbank.sh
filter_list.txt
/src/assets/data_package.json.gz
__pycache__
# BAM files are too large to track for example data
example_data_genbank/*/bam/**
# Don't need to track redundant fasta_processed files
example_data_genbank/*/fasta_processed/**
# Case_data and data_complete files are too large in RSV
case_data.*
data_complete.*
**/.snakemake_timestamp
example_data_genbank/*/status/**
example_data_genbank/*/lineage_treetime/*.txt
example_data_genbank/*/lineage_treetime/*.png
example_data_genbank/*/lineage_treetime/*.pdf
data
data_genbank
example_data_genbank/rsv/**
example_data_genbank/flu/**
example_data_genbank/sars2/**
data_flu_gisaid_small/**
data_flu_genbank_small/**
# scratch notebooks
workflow_main/notebooks/**
workflow_main/scripts/*.csv
# SnapGene - temp files
static_data/flu/alignments/.sglock/**
# MOTD
MOTD*.html