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
#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
#3172 - Comment in 'nf-core create-params-file --show-hidden' indicates hidden parameters are missing. Params are there
Issue -
State: open - Opened by FriederikeHanssen 15 days ago
Labels: bug
#3171 - Template: add option to exclude the workflows directory from pipeline template
Pull Request -
State: open - Opened by mirpedrol 15 days ago
#3169 - exclude CITATIONS.md file when excluding citations from pipeline template
Pull Request -
State: open - Opened by mirpedrol 15 days ago
#3168 - Remove if/else block to include `igenomes.config` and add `igenomes_ignored.config`
Pull Request -
State: open - Opened by mirpedrol 15 days ago
#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
#3158 - nf-core pipelines bump-version command should update pipeline version in nf-test snapshots
Issue -
State: open - Opened by maxulysse 27 days ago
Labels: enhancement
#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
#3147 - Linting: handle cases where the directory path contains the name of the component
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
#3128 - Template: add option to exclude nf-core components from pipeline template
Pull Request -
State: closed - Opened by mirpedrol about 1 month ago
#3127 - Template: add option to exclude adaptivecard and slackreport 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
#3113 - GHA using the template features yaml file was not working as expected [skip changelog]
Pull Request -
State: closed - Opened by mirpedrol about 2 months ago
#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
#3109 - `nf-core sync` does not respect existing template config on dev branch
Issue -
State: open - Opened by awgymer about 2 months ago
#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
#3099 - Template: Add tests to ensure all files are part of a template customisation group and all groups are tested
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
#3088 - Manual include or exclude specific files in template
Issue -
State: open - Opened by adamrtalbot 2 months ago
#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
#3084 - Template: add option to exclude code linters for custom pipeline template
Pull Request -
State: closed - Opened by mirpedrol 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