Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nf-core/tools issues and pull requests

#3304 - Remove toList() channel operation from inside onComplete block

Pull Request - State: open - Opened by robsyme about 2 months ago

#3303 - Conda install nf-core cli on mac arm64 fails

Issue - State: open - Opened by swingingsimian about 2 months ago
Labels: bug

#3302 - Improve documentation writing

Pull Request - State: open - Opened by LouisLeNezet about 2 months ago - 1 comment

#3301 - Move modules config import

Pull Request - State: closed - Opened by LouisLeNezet about 2 months ago - 1 comment
Labels: bug, template

#3300 - Include config `modules.config` in the wrong place ?

Issue - State: closed - Opened by LouisLeNezet about 2 months ago - 2 comments
Labels: bug

#3299 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0

Pull Request - State: closed - Opened by renovate[bot] about 2 months ago - 1 comment

#3298 - Improve subworkflow nf-test migration warning

Pull Request - State: open - Opened by edmundmiller about 2 months ago - 1 comment

#3297 - `nf-core subworkflows lint` nf-test directory is missing rule is inconsistent

Issue - State: open - Opened by edmundmiller about 2 months ago - 1 comment
Labels: bug

#3296 - Template: Remove `def` from `nextflow.config` and add `trace_report_suffix` param

Pull Request - State: closed - Opened by mirpedrol about 2 months ago - 1 comment

#3295 - Cleanup needed for nf-core logo / monochrome logs.

Issue - State: closed - Opened by ewels about 2 months ago - 2 comments
Labels: template

#3294 - Fix final language server errors in template

Issue - State: closed - Opened by ewels about 2 months ago - 2 comments
Labels: template

#3293 - Download: Seqera containers Patch 2

Pull Request - State: open - Opened by MatthiasZepper about 2 months ago - 1 comment

#3292 - build: Setup VS Code tests

Pull Request - State: open - Opened by edmundmiller about 2 months ago - 3 comments

#3291 - Fix usage of cache path and implement parallized testing

Pull Request - State: open - Opened by mashehu about 2 months ago
Labels: WIP

#3289 - Add `manifest.contributors` to template

Issue - State: open - Opened by ewels about 2 months ago
Labels: template, enhancement

#3288 - Lint pipelines nextflow schema against the meta schema

Issue - State: open - Opened by mirpedrol about 2 months ago
Labels: template, pipeline-testing, schema, enhancement

#3287 - Documentation shows the old commands without `pipelines` prefix

Issue - State: open - Opened by mirpedrol about 2 months ago
Labels: bug, documentation

#3285 - download pipelines fails with some seqera containers

Issue - State: open - Opened by znorgaard 2 months ago - 4 comments
Labels: bug, download

#3284 - Update python:3.12-slim Docker digest to 2a6386a

Pull Request - State: closed - Opened by renovate[bot] 2 months ago - 1 comment

#3283 - Update codecov/codecov-action action to v5

Pull Request - State: closed - Opened by renovate[bot] 2 months ago - 1 comment

#3282 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4

Pull Request - State: closed - Opened by renovate[bot] 2 months ago - 2 comments

#3281 - linting fails to execute if "----" present in module patch diff file

Issue - State: open - Opened by znorgaard 2 months ago
Labels: bug

#3279 - General: Add hint to solve git errors with a synced repo

Pull Request - State: closed - Opened by mirpedrol 2 months ago - 1 comment

#3278 - Allow skipping linting of specific subworkflows

Issue - State: open - Opened by mirpedrol 2 months ago
Labels: linting, good-first-issue, enhancement

#3276 - handle new schema structure in `nf-core pipelines create-params-file`

Pull Request - State: closed - Opened by mashehu 2 months ago - 1 comment

#3275 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3

Pull Request - State: closed - Opened by renovate[bot] 2 months ago - 1 comment

#3274 - Gitpod miniforge

Pull Request - State: closed - Opened by mahesh-panchal 2 months ago - 2 comments

#3273 - Single qutation mark ' in a comment makes AWS release full test break

Issue - State: open - Opened by jannikseidelQBiC 2 months ago - 2 comments
Labels: bug

#3272 - Template: Add `gpu` profile

Pull Request - State: open - Opened by mashehu 2 months ago - 12 comments

#3271 - template: add `gpu` profile

Pull Request - State: closed - Opened by mashehu 2 months ago - 3 comments

#3270 - Phase out the `when` directive

Issue - State: open - Opened by nictru 3 months ago
Labels: enhancement

#3269 - Update base to use new previous task

Issue - State: open - Opened by edmundmiller 3 months ago

#3268 - Fix typo

Pull Request - State: closed - Opened by SPPearce 3 months ago - 1 comment

#3267 - Fix logo typo in help message for create logos

Pull Request - State: closed - Opened by jfy133 3 months ago - 2 comments

#3263 - Un-informative error message from strange linting runs

Issue - State: closed - Opened by fasterius 3 months ago - 1 comment
Labels: bug

#3262 - nf-core pipeline lint gives cryptic prettier error message

Issue - State: open - Opened by marrip 3 months ago - 7 comments
Labels: bug

#3261 - create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools

Pull Request - State: open - Opened by Joon-Klaps 3 months ago - 1 comment

#3260 - 3257 - Add linkify version to fix bioconda dependencies

Pull Request - State: closed - Opened by pmoris 3 months ago - 3 comments

#3258 - Provide novel tooling for regulatory needs

Issue - State: open - Opened by apeltzer 3 months ago - 1 comment
Labels: enhancement, regulatory

#3257 - ModuleNotFoundError for nf-core v3.0.2 installed from bioconda

Issue - State: closed - Opened by pmoris 3 months ago - 4 comments
Labels: bug

#3256 - 1929: local modules use remote format from template

Pull Request - State: open - Opened by awgymer 3 months ago - 2 comments

#3255 - Template: Add resource limits to Gitpod profile

Pull Request - State: closed - Opened by mahesh-panchal 3 months ago - 4 comments

#3254 - Pipeline creation should specify branch name when initialising git repository

Issue - State: open - Opened by alexlyttle 3 months ago
Labels: enhancement

#3253 - nf-core pipelines bump-versions doesn't update .nf-core.yml

Issue - State: closed - Opened by jfy133 3 months ago - 2 comments
Labels: bug

#3252 - Template fails linting/pre-commit

Issue - State: closed - Opened by alexlyttle 3 months ago - 1 comment
Labels: bug

#3251 - nf-core modules create tool/subtool should make a main.nf in a subfolder of subtool in pipelines

Issue - State: closed - Opened by mahesh-panchal 3 months ago - 2 comments
Labels: enhancement

#3250 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1

Pull Request - State: closed - Opened by renovate[bot] 3 months ago - 2 comments

#3249 - chore(deps): update github actions

Pull Request - State: closed - Opened by renovate[bot] 3 months ago - 1 comment

#3248 - Modules meta.yml differentiate between tuple and single element channels

Issue - State: open - Opened by mirpedrol 3 months ago
Labels: bug, linting, modules

#3247 - add `--dir/-d` option to schema commands

Pull Request - State: closed - Opened by mashehu 3 months ago - 4 comments

#3246 - Modules: add a panel around diff previews when updating

Pull Request - State: closed - Opened by mashehu 3 months ago - 9 comments

#3245 - nf-core pipelines bump-version doesn't consider skipped features

Issue - State: open - Opened by mashehu 3 months ago
Labels: bug

#3244 - Download: Seqera container support - Patch 1

Pull Request - State: closed - Opened by MatthiasZepper 3 months ago - 1 comment
Labels: download

#3243 - Adopt nf-test sharding

Issue - State: open - Opened by edmundmiller 3 months ago - 3 comments

#3242 - Seqera containers example

Pull Request - State: closed - Opened by pinin4fjords 3 months ago - 1 comment

#3241 - Remove defaults conda channel from pipeline template

Issue - State: closed - Opened by ktmeaton 3 months ago - 3 comments

#3239 - Add a separater between each module's set of diffs during 'preview changes' during module updates

Issue - State: open - Opened by jfy133 3 months ago - 1 comment
Labels: enhancement

#3237 - Update GitHub Actions

Pull Request - State: closed - Opened by renovate[bot] 3 months ago

#3228 - allow mixed str and dict in lint config

Pull Request - State: open - Opened by mashehu 3 months ago - 1 comment
Labels: WIP

#3219 - Dev -> main for 3.0.2

Pull Request - State: closed - Opened by mashehu 3 months ago - 1 comment

#3218 - Template: fix pre-commit lining failing on pipelines template

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3216 - bump version to 3.0.2 [skip changelog]

Pull Request - State: closed - Opened by mirpedrol 3 months ago - 1 comment

#3215 - Use updated pipeline commands in docstrings

Pull Request - State: closed - Opened by mashehu 3 months ago

#3214 - TEMPLATE: Parallelize pipeline GHA tests over docker/conda/singularity

Pull Request - State: closed - Opened by maxulysse 3 months ago - 7 comments

#3213 - Linting: Fix bug when linting schema params

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3212 - TEMPLATE: Fix version comment action

Pull Request - State: closed - Opened by mashehu 3 months ago - 3 comments

#3211 - bump version to 3.0.2dev

Pull Request - State: closed - Opened by mashehu 3 months ago

#3210 - mev -> main for 3.0.1

Pull Request - State: closed - Opened by mashehu 3 months ago

#3209 - CI: fix artifact upload of snapshot report

Pull Request - State: closed - Opened by mashehu 3 months ago

#3208 - update nf-core subworkflows [skip changelog]

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3207 - Bump version to 3.0.1

Pull Request - State: closed - Opened by mashehu 3 months ago - 2 comments

#3206 - fix more jinja newlines

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3205 - Use correct key for parsing `defaultIgnoreParams`

Pull Request - State: closed - Opened by mashehu 3 months ago

#3204 - fix too many empty lines added to .editorconfig file

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3203 - Template: run awsfulltest only when target branch is `master`

Pull Request - State: closed - Opened by mashehu 3 months ago

#3202 - Fix a typo in the linting action

Pull Request - State: closed - Opened by nvnieuwk 3 months ago - 1 comment

#3201 - Fix comment section headers so they don't give phantom merge conflict warnings

Pull Request - State: closed - Opened by jfy133 3 months ago - 7 comments

#3200 - Dev -> main

Pull Request - State: closed - Opened by mashehu 3 months ago - 1 comment

#3199 - Release review [skip changelog]

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3198 - `master` -> `main`

Pull Request - State: closed - Opened by mashehu 3 months ago

#3197 - Dev -> Master for v3.0.0

Pull Request - State: closed - Opened by mirpedrol 3 months ago - 1 comment

#3196 - bump version to 3.0.0

Pull Request - State: closed - Opened by mirpedrol 3 months ago

#3195 - fix whitespaces in rendered template

Pull Request - State: closed - Opened by mashehu 3 months ago

#3194 - add pipeline name as an optional sync input

Pull Request - State: closed - Opened by mashehu 3 months ago

#3193 - Update python:3.12-slim Docker digest to af4e85f

Pull Request - State: closed - Opened by renovate[bot] 4 months ago

#3192 - Vscode settings

Pull Request - State: closed - Opened by ewels 4 months ago - 8 comments

#3191 - TEMPLATE: Add null/ to .gitignore

Pull Request - State: closed - Opened by maxulysse 4 months ago - 1 comment

#3190 - fix template new lines

Pull Request - State: closed - Opened by mirpedrol 4 months ago

#3189 - add API docs for .nf-core.yml

Pull Request - State: closed - Opened by mashehu 4 months ago