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cg

Glue between Clinical Genomics apps

https://github.com/clinical-genomics/cg

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary

Keywords from Contributors

bioinformatics reporting typing workflows pipelines nextflow autograd nf-core clinical microbial
Last synced: 10 months ago · JSON representation

Repository

Glue between Clinical Genomics apps

Basic Info
  • Host: GitHub
  • Owner: Clinical-Genomics
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 36.7 MB
Statistics
  • Stars: 9
  • Watchers: 10
  • Forks: 3
  • Open Issues: 108
  • Releases: 1,000
Created over 9 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing Codeowners

README.md

cg

Build Status - Github Coverage Status GitHub issues-closed Average time to resolve an issue Percentage of issues still open CodeFactor Code style: black

cg stands for Clinical Genomics; a clinical sequencing platform under SciLifeLab

In this context, cg provides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:

Contributing

Please check out our guide for contributing to cg

Installation

Cg written in Python 3.9+ and is available on the Python Package Index (PyPI).

bash pip install cg

If you would like to install the latest development version, use poetry.

bash git clone https://github.com/Clinical-Genomics/cg cd cg poetry install

For development, use poetry install --all-extras to install development dependencies.

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 4,046
  • Total Committers: 66
  • Avg Commits per committer: 61.303
  • Development Distribution Score (DDS): 0.75
Past Year
  • Commits: 1,273
  • Committers: 25
  • Avg Commits per committer: 50.92
  • Development Distribution Score (DDS): 0.501
Top Committers
Name Email Commits
Patrik Grenfeldt p****t@s****e 1,011
Clinical Genomics Bot c****m@g****m 856
Robin Andeer r****r@g****m 420
Måns Magnusson m****n@s****e 202
Sebastian Allard s****d@s****e 197
Kenny Billiau k****u@s****e 145
Henrik Stranneheim h****m@s****e 133
Mropat m****t@g****m 121
Maria Ropat 3****t 108
Vincent Janvid 6****v 101
ChristianOertlin c****n@s****e 100
barrystokman b****n@g****m 84
Barry Stokman 2****n 59
mayabrandi m****i@s****e 55
Isak Ohlsson Ångnell 4****n 47
Sebastian Diaz j****a@s****e 47
ivadym v****k@s****e 42
Eva C 2****c 41
Karl Nyrén 4****r 36
Henning Onsbring 6****g 28
northwestwitch r****a@g****m 23
adrosenbaum 4****m 17
Gustav Lagneborg 1****b 11
Anders Jemt j****n 11
Hassan Foroughi h****a 10
Emma Sernstad e****d@s****e 10
Sofia Stamouli 9****m 9
Peter Pruisscher 5****u 9
Maya Brandi m****i@1****l 8
Daniel Nilsson d****n@g****m 8
and 36 more...
Committer Domains (Top 20 + Academic)
scilifelab.se: 18 130-229-14-63-dhcp.wlan.ki.se: 1 130-229-10-135-dhcp.wlan.ki.se: 1 130-229-1-241-dhcp.wlan.ki.se: 1 130-229-7-47-dhcp.wlan.ki.se: 1 130-229-12-205-dhcp.wlan.ki.se: 1 130-229-13-56-dhcp.wlan.ki.se: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 637
  • Total pull requests: 1,864
  • Average time to close issues: 5 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 47
  • Total pull request authors: 34
  • Average comments per issue: 1.84
  • Average comments per pull request: 1.89
  • Merged pull requests: 1,332
  • Bot issues: 1
  • Bot pull requests: 23
Past Year
  • Issues: 219
  • Pull requests: 607
  • Average time to close issues: 22 days
  • Average time to close pull requests: 6 days
  • Issue authors: 22
  • Pull request authors: 23
  • Average comments per issue: 0.68
  • Average comments per pull request: 1.33
  • Merged pull requests: 412
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • Vince-janv (98)
  • seallard (80)
  • diitaz93 (63)
  • islean (57)
  • karlnyr (56)
  • fevac (38)
  • beatrizsavinhas (38)
  • ChrOertlin (34)
  • ivadym (16)
  • Karl-Svard (15)
  • henrikstranneheim (13)
  • RasmusBurge-CG (12)
  • mathiasbio (11)
  • peterpru (9)
  • jemten (9)
Pull Request Authors
  • islean (386)
  • seallard (302)
  • diitaz93 (252)
  • ChrOertlin (229)
  • henrikstranneheim (132)
  • Vince-janv (116)
  • rannick (60)
  • fevac (54)
  • ivadym (52)
  • peterpru (47)
  • beatrizsavinhas (41)
  • sofstam (31)
  • karlnyr (27)
  • eliottBo (24)
  • dependabot[bot] (23)
Top Labels
Issue Labels
Bug (109) Needs Refinement (74) Effort S (55) Gain M (40) Urgency S (38) Urgency L (34) Effort M (34) Gain L (33) Urgency M (30) demultiplex (24) Project Task (22) Gain S (21) rnafusion (18) Enhancement (14) cg (13) backend (11) on hold (10) Refactor (10) feature (9) Balsamic (9) Good first issue (9) technical-debt (6) production (6) Effort L (6) security (5) customer-experience (5) nallo (4) Prod Suitable (4) mip-rna (4) developer-experience (3)
Pull Request Labels
Project Task (69) Enhancement (40) Bug (27) demultiplex (24) dependencies (24) raredisease (22) alembic migration (20) cg (19) nallo (17) taxprofiler (13) rnafusion (7) security (6) Needs Refinement (5) Effort S (3) Urgency S (3) Gain M (3) Refactor (3) Streamline Delivery (3) bioinfo-dev (3) Urgency L (3) technical-debt (2) Gain L (2) Effort M (2) on hold (2) Urgency M (2) customer-experience (1) production (1) Scout (1) Customer request (1) backend (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 30,024 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1,986
  • Total maintainers: 4
  • Total advisories: 1
pypi.org: cg

Clinical Genomics command center

  • Versions: 1,986
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 30,024 Last month
Rankings
Downloads: 3.2%
Dependent packages count: 10.1%
Average: 14.9%
Forks count: 19.1%
Stargazers count: 20.4%
Dependent repos count: 21.5%
Maintainers (4)
henriks karlnyr clingen Vince-janv
Advisories (1)
Last synced: 10 months ago

Dependencies

requirements-dev.txt pypi
  • docutils *
  • mock *
  • pytest >=5.2
  • pytest-mock *
  • snapshottest *
requirements.txt pypi
  • Alchy *
  • Click <7.0
  • Flask >=1.1.1
  • Flask-Admin *
  • Flask-Alchy *
  • Flask-CORS *
  • Flask-Dance *
  • Flask-SQLAlchemy ==2.1
  • SQLAlchemy <1.4
  • alive_progress *
  • ansi *
  • blinker *
  • cgmodels >=0.10.1
  • coloredlogs *
  • email-validator *
  • genologics *
  • google-auth *
  • gunicorn *
  • housekeeper >=2.5
  • lxml *
  • markupsafe <2.1
  • marshmallow >3
  • openpyxl *
  • packaging *
  • pandas *
  • paramiko *
  • petname *
  • pydantic *
  • pymysql *
  • python-dateutil *
  • pyyaml *
  • requests *
  • requests_cache *
  • sendmail-container *
  • setuptools >=39.2.0
  • tabulate *
  • typing_extensions *
  • werkzeug <1.0.0
  • wtforms <3.0.0
.github/workflows/black.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • psf/black stable composite
.github/workflows/build_and_publish.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/build_dockerfile_on_push.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v3 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
.github/workflows/build_dockerfile_on_release.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v3 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
.github/workflows/bumpversion.yml actions
  • Clinical-Genomics/bump2version-ci v3 composite
.github/workflows/deploy_prod.yml actions
.github/workflows/deploy_stage.yml actions
.github/workflows/installations.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/tests_and_coverage.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • coverallsapp/github-action 1.1.3 composite
Dockerfile docker
  • docker.io/library/python 3.7-slim-bullseye build
pyproject.toml pypi
setup.py pypi