nf-core/tools

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

Stars: 322
Forks: 255
Open beginner issues: 0
Indexed issues: 357
Avg merge: 2d 3h
Merged PRs (30d): 5

Dominant language: Python
License: MIT
Last GitHub push: Jul 29, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue

Beginner friendly Everything

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357 open issues indexed

Lint: warn when a docs page will not be rendered on the website Open

nf-core/tools#4474 · 1 assignee · Opened Sep 19, 2026
Reduce privileged-token exposure in fix_linting.yml Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/tools#4471 · Opened Sep 16, 2026
nf-core/tools: EDAM ontology map covers 61 of 728 format concepts, and a failed download is indistinguishable from "no term exists" Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

nf-core/tools#4468 · Opened Sep 11, 2026
Malformed or missing manifest.name gives opaque error / IndexError instead of a lint failure Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nf-core/tools#4467 · 1 comment · Opened Sep 10, 2026
API reference pages are not available Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/tools#4465 · Opened Sep 4, 2026
IndexError: string index out of range Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/tools#4464 · Opened Sep 4, 2026
missing build_id value Open

awaiting-feedback bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/tools#4458 · 2 comments · Opened Aug 31, 2026
Missing corresponding arm build Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/tools#4457 · Opened Aug 31, 2026
Add support to Apple container Open

enhancement

nf-core/tools#4456 · 1 assignee · Opened Aug 26, 2026
Formatting issues when generating container definitions Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

nf-core/tools#4452 · Opened Aug 21, 2026
`nf-core pipelines lint` silently suppresses all module linting on error. Open

bug

nf-core/tools#4447 · 4 comments · 1 assignee · Opened Aug 19, 2026
Action Required: Fix Renovate Configuration Open

nf-core/tools#4446 · 2 comments · 1 assignee · Opened Aug 18, 2026
Add linting to flag outdir being set in test_full or test Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/tools#4440 · 1 comment · Opened Aug 6, 2026
[request] Lint for a potential runtime error with nf-test and github actions Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/tools#4419 · Opened Jul 28, 2026
Lint error: `KeyError: 'manifest.name'` with contributor ORCiD Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/tools#4416 · 1 comment · 2 reactions · Opened Jul 23, 2026
`--plain-text` for `test` commands Open

enhancement

nf-core/tools#4372 · 1 assignee · Opened Jul 3, 2026
Pull online test-datasets with `nf-core pipelines download` Open

download enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/tools#4370 · Opened Jul 2, 2026
Ro-crate path to file not being automatically updated Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/tools#4369 · Opened Jul 2, 2026
Schema validation parses string incorrectly if they're quoted integers Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 58/100

nf-core/tools#4367 · Opened Jul 1, 2026
Linting or GHA to test whether all modules of a module suite are updated Open

enhancement linting modules

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/tools#4355 · 1 comment · Opened Jun 26, 2026
Auto-updated markdown table of default resource requests in pipeline template Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 48/100

nf-core/tools#4345 · 6 comments · 3 reactions · Opened Jun 24, 2026
Consider enforcing line feeds in .gitattributes Open

enhancement

Difficulty 1/5 Under an hour Newbie friendliness 85/100

nf-core/tools#4341 · Opened Jun 23, 2026
Validate output files using the new output syntax in documentation Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/tools#4336 · 1 reaction · Opened Jun 18, 2026
Keep the citations file in sync with installed modules (nf-core/tools lint) Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/tools#4328 · Opened Jun 16, 2026
Incorrect if-statement logic in nf-core modules test output Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

nf-core/tools#4327 · 4 comments · Opened Jun 16, 2026
Investigate reducing base container size for wave provisioned containers. Open

infrastructure

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/tools#4315 · Opened Jun 5, 2026
Check for dead links in the template during linting Open

enhancement

nf-core/tools#4308 · 1 assignee · Opened May 28, 2026
User-selected branch used for upstream repo when updating modules from a forked subworkflow remote Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/tools#4296 · Opened May 23, 2026
Add option to disable creating container configs Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/tools#4295 · 1 comment · Opened May 23, 2026
stack trace using nf-core modules test Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/tools#4273 · Opened May 8, 2026
Handle deprecated and deleted modules/subworkflows gracefully Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/tools#4260 · 1 reaction · Opened May 5, 2026
meta.json stub file trips up meta_nf_meta_key linting Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nf-core/tools#4250 · 5 comments · Opened Apr 29, 2026
stub `.gz` linting is too restrictive Open

bug good-first-issue

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

nf-core/tools#4231 · 2 comments · Opened Apr 28, 2026
Fetch pipeline config in JSON Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

nf-core/tools#4204 · Opened Apr 20, 2026
Patch file is removed when previewing an update diff Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/tools#4183 · Opened Apr 10, 2026
modules.json - inconsistent formatting across functions Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 66/100

nf-core/tools#4177 · 2 comments · Opened Apr 7, 2026
Update lint checks for `modules_testdata_base_path` and `pipelines_testdata_base_path` Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/tools#4176 · Opened Apr 7, 2026
Error install subworkflow with specific module Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 58/100

nf-core/tools#4173 · Opened Apr 4, 2026
Make `utils_nfcore_<pipeline>_pipeline` subworkflow nf-core linting compliant or don't lint file Open

bug linting

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/tools#4157 · Opened Mar 31, 2026
Using strict syntax causes template to raise an error when setting boolean options on CLI Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nf-core/tools#4100 · 9 comments · Opened Mar 11, 2026
Configbuilder: _detect_module_system() and _get_container_systems() don't work as expected. Open

bug

nf-core/tools#4098 · 1 comment · 1 assignee · Opened Mar 11, 2026
Allow aliasing of git remotes with short names Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/tools#4096 · 3 comments · Opened Mar 6, 2026
Configbuilder: Automated process detection Open

command line tools enhancement

nf-core/tools#4089 · 1 assignee · Opened Mar 5, 2026
Configbuilder: refactor & clean up code Open

command line tools enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/tools#4088 · Opened Mar 5, 2026
Configbuilder: testing automated infrastructure system detection Open

command line tools enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/tools#4087 · Opened Mar 5, 2026
Cannot patch subworkflows if you include a function in it Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nf-core/tools#4084 · 2 comments · Opened Mar 5, 2026
nf-core subworkflows lint isn't comparing output channels between the main.nf and meta.yml Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/tools#4066 · 1 comment · Opened Feb 27, 2026
Linting: multi line tuple is interpreted as multiple inputs Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/tools#4062 · Opened Feb 27, 2026
Workflow handlers deprecated Open

enhancement high-priority template

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/tools#4060 · 6 comments · Opened Feb 26, 2026
Renovate uv stuff Open

nf-core/tools#4057 · 2 assignees · Opened Feb 24, 2026

nf-core/tools

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