nf-core

Python package with helper tools for the nf-core community.

https://github.com/nf-core/tools

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
22 of 137 committers (16.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (17.2%) to scientific vocabulary

Keywords

bioinformatics linter linting nextflow nf-core pipeline python workflow

Keywords from Contributors

workflows pipelines nf-test dsl2 metagenomics rna-seq epigenome rna annotation illumina

Last synced: 6 months ago · JSON representation ·

Repository

Python package with helper tools for the nf-core community.

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Python
Default Branch: main
Homepage: https://nf-co.re
Size: 17.7 MB

Statistics

Stars: 265
Watchers: 165
Forks: 208
Open Issues: 323
Releases: 59

Topics

bioinformatics linter linting nextflow nf-core pipeline python workflow

Created about 8 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

README.md

A python package with helper tools for the nf-core community.

The nf-core tools package is written in Python and can be imported and used within other packages. For documentation of the internal Python functions, please refer to the Tools Python API docs.

Installation

For full installation instructions, please see the nf-core documentation. Below is a quick-start for those who know what they're doing:

Bioconda

Install from Bioconda:

bash conda install nf-core

Alternatively, you can create a new environment with both nf-core/tools and nextflow:

bash conda create --name nf-core python=3.13 nf-core nextflow conda activate nf-core

Python Package Index

Install from PyPI:

bash pip install nf-core

Development version

bash pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev

If editing, fork and clone the repo, then install as follows:

bash pip install --upgrade -r requirements-dev.txt -e .

Contributions and Support

If you would like to contribute to this package, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #tools channel (you can join with this invite).

Citation

If you use nf-core tools in your work, please cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

Name: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
authors:
  - family-names: Ewels
    given-names: Philip
  - family-names: Peltzer
    given-names: Alexander
  - family-names: Fillinger
    given-names: Sven
  - family-names: Patel
    given-names: Harshil
  - family-names: Alneberg
    given-names: Johannes
  - family-names: Wilm
    given-names: Andreas
  - family-names: Garcia
    given-names: Maxime Ulysse
  - family-names: Di Tommaso
    given-names: Paolo
  - family-names: Nahnsen
    given-names: Sven
title: "The nf-core framework for community-curated bioinformatics pipelines."
version: 2.4.1
doi: 10.1038/s41587-020-0439-x
date-released: 2022-05-16
url: https://github.com/nf-core/tools
preferred-citation:
  type: article
  authors:
    - family-names: Ewels
      given-names: Philip
    - family-names: Peltzer
      given-names: Alexander
    - family-names: Fillinger
      given-names: Sven
    - family-names: Patel
      given-names: Harshil
    - family-names: Alneberg
      given-names: Johannes
    - family-names: Wilm
      given-names: Andreas
    - family-names: Garcia
      given-names: Maxime Ulysse
    - family-names: Di Tommaso
      given-names: Paolo
    - family-names: Nahnsen
      given-names: Sven
  doi: 10.1038/s41587-020-0439-x
  journal: nature biotechnology
  start: 276
  end: 278
  title: "The nf-core framework for community-curated bioinformatics pipelines."
  issue: 3
  volume: 38
  year: 2020
  url: https://dx.doi.org/10.1038/s41587-020-0439-x

Committers

Last synced: about 2 years ago

All Time

Total Commits: 6,859
Total Committers: 137
Avg Commits per committer: 50.066
Development Distribution Score (DDS): 0.769

Past Year

Commits: 1,082
Committers: 52
Avg Commits per committer: 20.808
Development Distribution Score (DDS): 0.745

Top Committers

Name	Email	Commits
Phil Ewels	p**s@s**e	1,587
mirpedrol	m**a@g**m	746
Erik Danielsson	d**0@g**m	549
drpatelh	d**l@g**m	531
kevinmenden	k**n@t**e	444
mashehu	m**3@g**m	371
Sven Fillinger	s**r@q**e	318
fabianegli	f**i@p**h	218
Harshil Patel	d**h@g**m	199
ggabernet	g**t@q**e	118
MaxUlysse	m**a@g**m	105
James A. Fellows Yates	j**3@g**m	99
Arthur Gymer	2****r	98
Matthias Zepper	M****r	96
Mahesh Binzer-Panchal	m**l@n**e	92
JoseEspinosa	k**u@g**m	80
Alexander Peltzer	a**r@g**m	74
Fabian Egli	f****i	63
Adam Talbot	a**t@s**o	51
Júlia Mir Pedrol	j**a@j**e	49
kedhammar	a**r@s**e	42
Adrien Coulier	a**r@m**e	41
Gregor Sturm	m**l@g**e	41
Harshil Patel	d****h	37
github-actions[bot]	g****]	37
Erik Danielsson	5****n	37
Matthias Hörtenhuber	m****u	32
matthiasho	m**r@k**e	31
Phil Ewels	p**s@s**o	26
Anne Marie Noronha	a****4	25
and 107 more...

Committer Domains (Top 20 + Academic)

scilifelab.se: 6 qbic.uni-tuebingen.de: 6 seqera.io: 3 sanger.ac.uk: 2 student.uni-tuebingen.de: 2 posteo.net: 2 t-online.de: 1 crick.ac.uk: 1 protonmail.ch: 1 uni-tuebingen.de: 1 mailbox.org: 1 microsoft.com: 1 fa2k.net: 1 pixelgen.com: 1 libero.it: 1 ugent.be: 1 janelia.hhmi.org: 1 informatik.uni-tuebingen.de: 1 nbis.se: 1 nf-co.re: 1 julias-mbp.am10.uni-tuebingen.de: 1 pucp.edu.pe: 1 alexanders-mbp.am10.uni-tuebingen.de: 1 fu-berlin.de: 1 liverpool.ac.uk: 1 gis.a-star.edu.sg: 1 gmi.oeaw.ac.at: 1 ed.ac.uk: 1 univ-lille.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 559
Total pull requests: 1,623
Average time to close issues: 8 months
Average time to close pull requests: 19 days
Total issue authors: 152
Total pull request authors: 89
Average comments per issue: 1.74
Average comments per pull request: 1.59
Merged pull requests: 1,258
Bot issues: 3
Bot pull requests: 364

Past Year

Issues: 161
Pull requests: 623
Average time to close issues: 17 days
Average time to close pull requests: 8 days
Issue authors: 69
Pull request authors: 43
Average comments per issue: 0.65
Average comments per pull request: 1.59
Merged pull requests: 453
Bot issues: 0
Bot pull requests: 138

View more stats

Top Authors

Issue Authors

ewels (62)
mirpedrol (38)
adamrtalbot (30)
mahesh-panchal (24)
maxulysse (24)
jfy133 (23)
edmundmiller (19)
drpatelh (19)
mashehu (18)
fabianegli (13)
awgymer (12)
FriederikeHanssen (11)
apeltzer (9)
Emiller88 (9)
nvnieuwk (7)

Pull Request Authors

mashehu (376)
renovate[bot] (362)
mirpedrol (334)
maxulysse (59)
ewels (53)
MatthiasZepper (38)
jfy133 (33)
adamrtalbot (29)
awgymer (21)
edmundmiller (21)
nvnieuwk (19)
mahesh-panchal (17)
toniher (13)
LaurenceKuhl (12)
JulianFlesch (12)

Top Labels

Issue Labels

bug (214) enhancement (180) infrastructure (51) template (43) command line tools (30) linting (29) download (27) good-first-issue (25) modules (25) high-priority (16) schema (14) automation (13) documentation (13) nf-test (12) pipeline-testing (8) subworkflows (8) low-priority (6) question (6) awaiting-feedback (3) Stale (3) WIP (2) won't-fix (1)

Pull Request Labels

WIP (26) download (17) template (10) enhancement (10) bug (9) command line tools (6) linting (6) documentation (5) high-priority (4) awaiting-feedback (3) Stale (3) awaiting-changes (3) subworkflows (3) infrastructure (3) dependencies (2) schema (2) security (2) modules (2) nf-test (2) automation (1)

Packages

Total packages: 1
Total downloads:
- pypi 18,282 last-month
Total docker downloads: 27,048

Total dependent packages: 1
Total dependent repositories: 4
Total versions: 59
Total maintainers: 4

pypi.org: nf-core

Helper tools for use with nf-core Nextflow pipelines.

Homepage: https://github.com/nf-core/tools
Documentation: https://nf-core.readthedocs.io/
License: MIT
Latest release: 3.3.2
published 8 months ago

Versions: 59
Dependent Packages: 1
Dependent Repositories: 4
Downloads: 18,282 Last month
Docker Downloads: 27,048

Rankings

Docker downloads count: 1.4%

Downloads: 3.3%

Forks count: 4.0%

Average: 4.3%

Dependent packages count: 4.7%

Stargazers count: 5.0%

Dependent repos count: 7.5%

Maintainers (4)

sven1103 alneberg apeltzer ewels

Last synced: 6 months ago

Dependencies

.github/workflows/branch.yml actions

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Dockerfile docker

python 3.8.9-slim build

docs/api/requirements.txt pypi

Sphinx >=3.3.1
myst-parser *
sphinx_rtd_theme >=0.5.0
sphinxcontrib-napoleon *

requirements-dev.txt pypi

Sphinx * development
black * development
isort * development
myst_parser * development
pytest-cov * development
pytest-datafiles * development
requests-mock * development
requests_mock * development
sphinx-rtd-theme * development

requirements.txt pypi

GitPython *
click *
filetype *
galaxy-tool-util *
jinja2 *
jsonschema >=3.0
markdown >=3.3
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prompt_toolkit >=3.0.3
pytest >=7.0.0
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pyyaml *
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refgenie *
requests *
requests_cache *
rich >=10.7.0
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tabulate *

.github/workflows/clean-up.yml actions

actions/stale v7 composite

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nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan

nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml cpan

nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml cpan

nf_core/pipeline-template/pyproject.toml pypi

pyproject.toml pypi

setup.py pypi

nf_core/module-template/meta.yml cpan

nf_core/subworkflow-template/meta.yml cpan

nf_core/module-template/environment.yml pypi

nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml pypi

nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml pypi

nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml pypi