Ecosyste.ms: Issues

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GitHub / nf-core/tools issues and pull requests

#3179 - Download: Fix support for Seqera Community Containers

Issue - State: open - Opened by MatthiasZepper 7 days ago - 3 comments
Labels: bug, high-priority

#3178 - Changes to nf-core pipelines download CLI

Pull Request - State: open - Opened by MatthiasZepper 8 days ago

#3177 - bump nf-schema to v2.1.1 in the template

Pull Request - State: closed - Opened by nvnieuwk 11 days ago - 3 comments

#3176 - Strip hyphens from hashtags for mastodon compatibiluty

Pull Request - State: closed - Opened by jfy133 13 days ago - 4 comments

#3175 - Add ability to install a subworkflow composed nf-core and non-nfcore modules/subworkflows.

Issue - State: open - Opened by kenibrewer 13 days ago - 2 comments
Labels: high-priority, enhancement

#3174 - Add ability to install a nf-core module into a private module library

Issue - State: open - Opened by kenibrewer 13 days ago - 5 comments
Labels: high-priority, enhancement

#3173 - I get an error about the imp module in python12

Issue - State: closed - Opened by kojix2 14 days ago - 2 comments
Labels: bug

#3167 - Template: remove try-catch blocks from nextflow.config

Pull Request - State: open - Opened by mirpedrol 18 days ago - 1 comment

#3166 - Template: Update modules and and local subworkflow syntax

Pull Request - State: open - Opened by mirpedrol 18 days ago

#3165 - Remove `import` statements from pipeline template

Issue - State: open - Opened by ewels 19 days ago - 1 comment
Labels: template, high-priority

#3164 - Update gitpod.Dockerfile

Pull Request - State: closed - Opened by sateeshperi 23 days ago - 1 comment

#3163 - Container cache download

Pull Request - State: open - Opened by muffato 24 days ago - 2 comments
Labels: WIP, download

#3162 - Singularity container symlinks not consistently created

Issue - State: open - Opened by muffato 24 days ago
Labels: bug, download

#3161 - Don't test conda `environment.yml` `name` attribute

Pull Request - State: closed - Opened by ewels 25 days ago - 2 comments

#3160 - error_retry label not recognized as standard label for certain module structures

Issue - State: open - Opened by Felix-Kummer 25 days ago - 2 comments
Labels: bug, linting, good-first-issue

#3159 - Add --update-all flag to conda in Gitpod

Pull Request - State: closed - Opened by mahesh-panchal 26 days ago - 1 comment

#3157 - `modules update` with `patch` deletes files in `templates`

Issue - State: open - Opened by FriederikeHanssen 28 days ago - 1 comment
Labels: bug

#3156 - Fix issue where tool and subtool have the same name

Pull Request - State: closed - Opened by nvnieuwk 28 days ago - 1 comment

#3155 - Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3

Pull Request - State: open - Opened by renovate[bot] about 1 month ago - 1 comment

#3154 - Update dependency pytest-textual-snapshot to v1

Pull Request - State: open - Opened by renovate[bot] about 1 month ago - 1 comment

#3153 - Update dependency textual-dev to v1.6.1

Pull Request - State: open - Opened by renovate[bot] about 1 month ago - 1 comment

#3152 - Update dependency textual to v0.80.1

Pull Request - State: open - Opened by renovate[bot] about 1 month ago

#3151 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.2

Pull Request - State: open - Opened by renovate[bot] about 1 month ago - 1 comment

#3150 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.7

Pull Request - State: open - Opened by renovate[bot] about 1 month ago - 1 comment

#3149 - Template: test pipeline with conda and singularity on PRs to master

Pull Request - State: open - Opened by mirpedrol about 1 month ago

#3148 - run `nf-core lint --release` on PRs to master

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3146 - what is 'getGenomeAttribute' and how can we use igenomes without it?

Issue - State: closed - Opened by stevekm about 1 month ago - 10 comments
Labels: question

#3145 - Schema: Support multi-line text inputs

Issue - State: open - Opened by ewels about 1 month ago - 1 comment
Labels: schema

#3144 - Release PR (dev to master) does not fail with a pipeline still on dev version

Issue - State: closed - Opened by maxulysse about 1 month ago
Labels: bug

#3143 - fix syncing a pipeline from current directory

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3142 - Allow `main` as default channel

Pull Request - State: open - Opened by mashehu about 1 month ago

#3141 - Create pre-commit hooks

Pull Request - State: open - Opened by edmundmiller about 1 month ago - 2 comments

#3140 - Pass a list of modules/subworkflows(files) to nf-core modules lint

Issue - State: open - Opened by edmundmiller about 1 month ago
Labels: enhancement

#3139 - Adopt pyproject.toml

Pull Request - State: open - Opened by edmundmiller about 1 month ago - 2 comments

#3138 - Automating pytest migration

Pull Request - State: open - Opened by GallVp about 1 month ago
Labels: automation, nf-test

#3137 - organise changelog and bump version to 3.0.0dev

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3136 - Update gitpod

Pull Request - State: closed - Opened by mahesh-panchal about 1 month ago

#3135 - Add a linting test for the metro map

Issue - State: open - Opened by maxulysse about 1 month ago
Labels: enhancement

#3134 - Template: add option to exclude tower.yml from pipeline template

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

#3133 - Template: add option to exclude test configs from pipeline template

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3132 - Remove try-catch blocks around institutional configs

Issue - State: open - Opened by bentsherman about 1 month ago - 14 comments
Labels: template, high-priority

#3131 - Move igenomes config into pipeline code

Issue - State: open - Opened by bentsherman about 1 month ago - 3 comments
Labels: high-priority

#3130 - Template: add option to exclude documentation from pipeline template

Pull Request - State: closed - Opened by mirpedrol about 1 month ago - 5 comments

#3129 - Template: add option to exclude fastqc from pipeline template

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3126 - Template: add option to exclude email from pipeline template

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3125 - Template: add option to exclude license from pipeline template

Pull Request - State: closed - Opened by mirpedrol about 1 month ago

#3124 - Update python:3.12-slim Docker digest to 59c7332

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

#3123 - Add `-w`, `--fail-warned` option to `nf-core schema lint`

Issue - State: open - Opened by theJasonFan about 2 months ago
Labels: enhancement

#3122 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0

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

#3121 - Update dependency prompt_toolkit to <=3.0.47

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

#3120 - Add a verbose option for nf-core modules test

Pull Request - State: closed - Opened by LaurenceKuhl about 2 months ago

#3119 - Moved the verbose for nf-core modules test

Pull Request - State: closed - Opened by LaurenceKuhl about 2 months ago

#3118 - Move the verbose for nf-core modules test

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

#3117 - Schema: rewrite to run local only and handle newer schema versions

Pull Request - State: open - Opened by mashehu about 2 months ago - 1 comment
Labels: WIP

#3116 - nf-schema support

Pull Request - State: closed - Opened by nvnieuwk about 2 months ago - 5 comments

#3115 - Components: allow spaces at the betinning of include statements

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

#3114 - Lint for test data paths and produce a warning/error if the config map is used?

Issue - State: open - Opened by GallVp about 2 months ago
Labels: enhancement

#3112 - add templatefeatures.yml to python package

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

#3111 - nf-core/tools download error

Issue - State: closed - Opened by apeltzer about 2 months ago - 5 comments
Labels: bug

#3110 - MultiQC results not cacheable

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

#3108 - Template: handle template features with a yaml file

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

#3107 - modules linting: Check that version.yml has version of all items in `environment.yml`

Issue - State: open - Opened by mashehu about 2 months ago
Labels: linting, modules

#3106 - Print test directory path in output from `nf-core test`

Issue - State: open - Opened by erikrikarddaniel about 2 months ago
Labels: enhancement

#3105 - Template: add option to exclude codespaces from pipeline template

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

#3104 - Template: add option to exclude changelog from custom pipeline template

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

#3103 - Template: add option to exclude multiqc from pipeline template

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

#3102 - Add bot action to update textual snapshots and write bot documentation

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

#3101 - Template: add option to exclude citations for custom pipeline template

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

#3100 - Template: add option to exclude gitpod for custom pipeline template

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

#3098 - Test pipelines with Singularity & Conda

Issue - State: open - Opened by mirpedrol about 2 months ago - 1 comment
Labels: template, pipeline-testing, enhancement, infrastructure

#3097 - `xx` is present as an output in meta.yml but not in main.nf

Issue - State: closed - Opened by GallVp about 2 months ago - 1 comment
Labels: enhancement

#3096 - Components: Modules: allow multiline module input tuple

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

#3095 - Components: Modules : allow module lables between double quotes

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

#3094 - Pipelines: allow numbers in custom pipeline name

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

#3093 - Support version topic channels

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

#3092 - Update dependency textual to v0.76.0

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

#3091 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1

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

#3090 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.5

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

#3089 - Linting throws an error if hyphens appear in the name

Issue - State: closed - Opened by adamrtalbot 2 months ago - 5 comments
Labels: bug

#3087 - Fix module linting warning for process_high_memory

Pull Request - State: closed - Opened by GallVp 2 months ago

#3086 - Add process_high_memory to create/lint list

Issue - State: closed - Opened by GallVp 2 months ago - 1 comment
Labels: enhancement

#3085 - Add `--migrate_pytest` option to `nf-core test` command

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

#3083 - feat: Install subworkflows with modules from different remotes

Pull Request - State: open - Opened by jvfe 2 months ago - 4 comments
Labels: enhancement

#3082 - Move --migrate-pytest command to `module test` command group

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

#3081 - fix the nested list bug that makes email not be delivered

Pull Request - State: open - Opened by HaidYi 2 months ago - 11 comments

#3080 - Fail to send the completion email

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

#3079 - Update python:3.12-slim Docker digest to 740d94a

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