nf-core tools issues - Githubissues

nf-core / tools

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

https://nf-co.re

MIT License

232 stars 187 forks source link

issues

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Template: remove try-catch blocks from nextflow.config

#3167 mirpedrol opened 8 hours ago
0
Template: Update modules and and local subworkflow syntax

#3166 mirpedrol opened 12 hours ago
0
Remove `import` statements from pipeline template

#3165 ewels opened 2 days ago
1
Update gitpod.Dockerfile

#3164 sateeshperi closed 4 days ago
1
Container cache download

#3163 muffato opened 6 days ago
2
Singularity container symlinks not consistently created

#3162 muffato opened 6 days ago
0
Don't test conda `environment.yml` `name` attribute

#3161 ewels closed 1 week ago
2
error_retry label not recognized as standard label for certain module structures

#3160 Felix-Kummer opened 1 week ago
1
Add --update-all flag to conda in Gitpod

#3159 mahesh-panchal closed 1 week ago
1
nf-core pipelines bump-version command should update pipeline version in nf-test snapshots

#3158 maxulysse opened 1 week ago
0
`modules update` with `patch` deletes files in `templates`

#3157 FriederikeHanssen opened 1 week ago
1
Fix issue where tool and subtool have the same name

#3156 nvnieuwk closed 1 week ago
1
Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3

#3155 renovate[bot] opened 1 week ago
1
Update dependency pytest-textual-snapshot to v1

#3154 renovate[bot] opened 1 week ago
1
Update dependency textual-dev to v1.6.1

#3153 renovate[bot] opened 1 week ago
1
Update dependency textual to v0.79.1

#3152 renovate[bot] opened 1 week ago
0
Update pre-commit hook pre-commit/mirrors-mypy to v1.11.2

#3151 renovate[bot] opened 1 week ago
1
Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.5

#3150 renovate[bot] opened 1 week ago
1
Template: test pipeline with conda and singularity on PRs to master

#3149 mirpedrol opened 2 weeks ago
0
run `nf-core lint --release` on PRs to master

#3148 mirpedrol closed 1 week ago
0
Linting: handle cases where the directory path contains the name of the component

#3147 mirpedrol closed 2 weeks ago
0
what is 'getGenomeAttribute' and how can we use igenomes without it?

#3146 stevekm closed 2 weeks ago
10
Schema: Support multi-line text inputs

#3145 ewels opened 2 weeks ago
1
Release PR (dev to master) does not fail with a pipeline still on dev version

#3144 maxulysse closed 1 week ago
0
fix syncing a pipeline from current directory

#3143 mirpedrol closed 2 weeks ago
0
Allow `main` as default channel

#3142 mashehu opened 2 weeks ago
0
Create pre-commit hooks

#3141 edmundmiller opened 2 weeks ago
2
Pass a list of modules/subworkflows(files) to nf-core modules lint

#3140 edmundmiller opened 2 weeks ago
0
Adopt pyproject.toml

#3139 edmundmiller opened 2 weeks ago
2
Automating pytest migration

#3138 GallVp opened 3 weeks ago
0
organise changelog and bump version to 3.0.0dev

#3137 mirpedrol closed 3 weeks ago
0
Update gitpod

#3136 mahesh-panchal closed 3 weeks ago
0
Add a linting test for the metro map

#3135 maxulysse opened 3 weeks ago
0
Template: add option to exclude tower.yml from pipeline template

#3134 mirpedrol closed 2 weeks ago
1
Template: add option to exclude test configs from pipeline template

#3133 mirpedrol closed 2 weeks ago
0
Remove try-catch blocks around institutional configs

#3132 bentsherman opened 3 weeks ago
14
Move igenomes config into pipeline code

#3131 bentsherman opened 3 weeks ago
3
Template: add option to exclude documentation from pipeline template

#3130 mirpedrol closed 2 weeks ago
5
Template: add option to exclude fastqc from pipeline template

#3129 mirpedrol closed 2 weeks ago
0
Template: add option to exclude nf-core components from pipeline template

#3128 mirpedrol closed 2 weeks ago
0
Template: add option to exclude adaptivecard and slackreport from pipeline template

#3127 mirpedrol closed 3 weeks ago
0
Template: add option to exclude email from pipeline template

#3126 mirpedrol closed 3 weeks ago
0
Template: add option to exclude license from pipeline template

#3125 mirpedrol closed 3 weeks ago
0
Update python:3.12-slim Docker digest to 59c7332

#3124 renovate[bot] closed 3 weeks ago
2
Add `-w`, `--fail-warned` option to `nf-core schema lint`

#3123 theJasonFan opened 4 weeks ago
0
Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0

#3122 renovate[bot] closed 4 weeks ago
0
Update dependency prompt_toolkit to <=3.0.47

#3121 renovate[bot] opened 4 weeks ago
1
Add a verbose option for nf-core modules test

#3120 LaurenceKuhl closed 4 weeks ago
0
Moved the verbose for nf-core modules test

#3119 LaurenceKuhl closed 4 weeks ago
0
Move the verbose for nf-core modules test

#3118 LaurenceKuhl closed 4 weeks ago
1