.gitignore

# adapted from https://gist.github.com/2427167

# Numerous always-ignore extensions
*.diff
*.err
*.orig
*.log
*.rej
*.swo
*.swp
*.vi
*~
*.sass-cache

# OS or Editor folders
.DS_Store
Thumbs.db
.cache
.project
.settings
.tmproj
*.esproj
nbproject
*.sublime-project
*.sublime-workspace

# Dreamweaver added files
_notes
dwsync.xml

# Komodo
*.komodoproject
.komodotools

# Folders to ignore
.hg
.svn
.CVS
intermediate
publish
.idea

# build script local files
build/buildinfo.properties
build/config/buildinfo.properties

# project specific
config.cfg
hive_params
data/*.ncRNA
temp/*
log/*
# hive database
*_rnacentral_update
pipeline.png
# macfuse files
._*
.fuse_hidden*

# python
*.py[cod]

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

default.nix
env/
data/Caenorhabditis_elegans.WBcel235.87.chromosome.IV.dat
data/Homo_sapiens.GRCh38.87.chromosome.*.dat
data/Mus_musculus.GRCm38.87.chromosome.*.dat
data/pub/
luigi.cfg
logging.cfg
local.config
work/
.nextflow*
data/ensembl_*/*.dat
data/ensembl/*.dat
data/gencode/human-transcripts.gff3
.editorconfig
data/ensembl/excluded.txt
data/intact/intact.txt
*.nix
Procfile
nix
.vim
target/
bin/json2fasta
bin/split-ena
bin/expand-urs
bin/ftp-export
bin/kv
bin/precompute
bin/search-export
bin/json2dfasta
bin/expression-parse
stubs
.envrc
workflows/litscan/results
workflows/litscan/metadata/files
workflows/litscan/metadata/rfam
workflows/litscan/metadata/merged_metadata
workflows/litscan/backup
workflows/litscan/submit
singularity/*
.python-version
bin/bed-expander
.projections.json