|
1 | | -# Byte-compiled / optimized / DLL files |
2 | | -__pycache__/ |
3 | | -*.py[cod] |
4 | | -*$py.class |
5 | | - |
6 | | -# C extensions |
7 | | -*.so |
8 | | - |
9 | | -# Distribution / packaging |
10 | | -.Python |
11 | | -build/ |
12 | | -develop-eggs/ |
13 | | -dist/ |
14 | | -downloads/ |
15 | | -eggs/ |
16 | | -.eggs/ |
17 | | -lib64/ |
18 | | -parts/ |
19 | | -sdist/ |
20 | | -var/ |
21 | | -wheels/ |
22 | | -share/python-wheels/ |
23 | | -*.egg-info/ |
24 | | -.installed.cfg |
25 | | -*.egg |
26 | | -MANIFEST |
27 | | - |
28 | | -# PyInstaller |
29 | | -# Usually these files are written by a python script from a template |
30 | | -# before PyInstaller builds the exe, so as to inject date/other infos into it. |
31 | | -*.manifest |
32 | | -*.spec |
33 | | - |
34 | | -# Installer logs |
35 | | -pip-log.txt |
36 | | -pip-delete-this-directory.txt |
37 | | - |
38 | | -# Unit test / coverage reports |
39 | | -htmlcov/ |
40 | | -.tox/ |
41 | | -.nox/ |
42 | | -.coverage |
43 | | -.coverage.* |
44 | | -.cache |
45 | | -nosetests.xml |
46 | | -coverage.xml |
47 | | -*.cover |
48 | | -*.py,cover |
49 | | -.hypothesis/ |
50 | | -.pytest_cache/ |
51 | | -cover/ |
52 | | - |
53 | | -# Translations |
54 | | -*.mo |
55 | | -*.pot |
56 | | - |
57 | | -# Django stuff: |
58 | | -*.log |
59 | | -local_settings.py |
60 | | -db.sqlite3 |
61 | | -db.sqlite3-journal |
62 | | - |
63 | | -# Flask stuff: |
64 | | -instance/ |
65 | | -.webassets-cache |
66 | | - |
67 | | -# Scrapy stuff: |
68 | | -.scrapy |
69 | | - |
70 | | -# Sphinx documentation |
71 | | -docs/_build/ |
72 | | - |
73 | | -# PyBuilder |
74 | | -.pybuilder/ |
75 | | -target/ |
76 | | - |
77 | | -# Jupyter Notebook |
78 | | -.ipynb_checkpoints |
79 | | - |
80 | | -# IPython |
81 | | -profile_default/ |
82 | | -ipython_config.py |
83 | | - |
84 | | -# pyenv |
85 | | -# For a library or package, you might want to ignore these files since the code is |
86 | | -# intended to run in multiple environments; otherwise, check them in: |
87 | | -# .python-version |
88 | | - |
89 | | -# pipenv |
90 | | -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. |
91 | | -# However, in case of collaboration, if having platform-specific dependencies or dependencies |
92 | | -# having no cross-platform support, pipenv may install dependencies that don't work, or not |
93 | | -# install all needed dependencies. |
94 | | -#Pipfile.lock |
95 | | - |
96 | | -# poetry |
97 | | -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. |
98 | | -# This is especially recommended for binary packages to ensure reproducibility, and is more |
99 | | -# commonly ignored for libraries. |
100 | | -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control |
101 | | -poetry.lock |
102 | | - |
103 | | -# pdm |
104 | | -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. |
105 | | -#pdm.lock |
106 | | -# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it |
107 | | -# in version control. |
108 | | -# https://pdm.fming.dev/#use-with-ide |
109 | | -.pdm.toml |
110 | | - |
111 | | -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm |
112 | | -__pypackages__/ |
113 | | - |
114 | | -# Celery stuff |
115 | | -celerybeat-schedule |
116 | | -celerybeat.pid |
117 | | - |
118 | | -# SageMath parsed files |
119 | | -*.sage.py |
120 | | - |
121 | | -# Environments |
122 | | -.env |
123 | | -.venv |
124 | | -env/ |
125 | | -venv/ |
126 | | -ENV/ |
127 | | -env.bak/ |
128 | | -venv.bak/ |
129 | | - |
130 | | -# Spyder project settings |
131 | | -.spyderproject |
132 | | -.spyproject |
133 | | - |
134 | | -# Rope project settings |
135 | | -.ropeproject |
136 | | - |
137 | | -# mkdocs documentation |
138 | | -/site |
139 | | - |
140 | | -# mypy |
141 | | -.mypy_cache/ |
142 | | -.dmypy.json |
143 | | -dmypy.json |
144 | | - |
145 | | -# Pyre type checker |
146 | | -.pyre/ |
147 | | - |
148 | | -# pytype static type analyzer |
149 | | -.pytype/ |
150 | | - |
151 | | -# Cython debug symbols |
152 | | -cython_debug/ |
153 | | - |
154 | | -# PyCharm |
155 | | -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can |
156 | | -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore |
157 | | -# and can be added to the global gitignore or merged into this file. For a more nuclear |
158 | | -# option (not recommended) you can uncomment the following to ignore the entire idea folder. |
159 | | -#.idea/ |
160 | | - |
161 | | -# concessions to pixi |
162 | | -.pixi/ |
163 | | -src/ |
164 | | - |
165 | | -# nextflow stuff |
166 | | -.nextflow/ |
167 | | -work/ |
168 | | -results/ |
169 | | -.nfresume |
170 | | - |
171 | | -.nextflow.log* |
172 | | -trace.txt* |
173 | | -report.html.* |
174 | | -timeline.html* |
175 | | -report.html* |
176 | | -*.dot |
177 | | -*.png.* |
178 | | - |
179 | | -# macos stuff |
180 | | -._* |
181 | | -.DS_Store |
182 | | - |
183 | | -# bioinformatics files |
184 | | -*.fa* |
185 | | -*.gtf |
186 | | -*.bam* |
187 | | -*.gbk |
188 | | -*.bed |
189 | | -models/ |
190 | | -snpEff_cache/ |
191 | | -nextclade_datasets/ |
192 | | -input/ |
193 | | -inputs/ |
194 | | -data/ |
195 | | -fastq/ |
196 | | -fastqs/ |
197 | | -reads/ |
198 | | -ref/ |
199 | | -samples/ |
200 | | -sandbox/ |
201 | | -tmp/ |
202 | | -scratch/ |
203 | | -scratch*# pixi environments |
204 | | -.pixi |
205 | | -*.egg-info |
206 | | - |
207 | | -# pixi environments |
208 | | -.pixi |
209 | | - |
210 | | -# uv stuff |
211 | | -uv.lock |
212 | | - |
213 | | -# quarto stuff |
214 | | -/.quarto/ |
| 1 | +* |
| 2 | + |
| 3 | +# project root directory |
| 4 | +!LICENSE |
| 5 | +!README.md |
| 6 | +!justfile |
| 7 | +!Dockerfile |
| 8 | +!pyproject.toml |
| 9 | +!pixi.lock |
| 10 | +!uv.lock |
| 11 | +!_quarto.yml |
| 12 | +!.pre-commit-config.yaml |
| 13 | +!.gitignore |
| 14 | +!.gitattributes |
| 15 | +!main.nf |
| 16 | +!nextflow.config |
| 17 | + |
| 18 | +# nextflow workflows |
| 19 | +!/workflows |
| 20 | +!/workflows/*.nf |
| 21 | + |
| 22 | +# nextflow subworkflows |
| 23 | +!/subworkflows |
| 24 | +!/subworkflows/*.nf |
| 25 | + |
| 26 | +# nextflow modules |
| 27 | +!/modules |
| 28 | +!/modules/*.nf |
| 29 | + |
| 30 | +# nextflow configuration |
| 31 | +!/conf |
| 32 | +!/conf/*.config |
| 33 | +!/conf/*.yml |
| 34 | + |
| 35 | +# bin of executable scripts |
| 36 | +!/bin |
| 37 | +!/bin/*.py |
| 38 | + |
| 39 | +# groovy libraries |
| 40 | +!/lib |
| 41 | +!/lib/*.groovy |
| 42 | + |
| 43 | +# documentation |
| 44 | +!/docs |
| 45 | +!/docs/*.qmd |
| 46 | +!/docs/*.md |
| 47 | +!/docs/*.pdf |
| 48 | +!/docs/*.html.gz |
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