Ecosyste.ms: Issues

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GitHub / nf-core/tools issues and pull requests

#3087 - Fix module linting warning for process_high_memory

Pull Request - State: closed - Opened by GallVp 6 months ago

#3086 - Add process_high_memory to create/lint list

Issue - State: closed - Opened by GallVp 6 months ago - 1 comment
Labels: enhancement

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

Pull Request - State: closed - Opened by mashehu 6 months ago

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

Pull Request - State: open - Opened by jvfe 6 months ago - 7 comments
Labels: enhancement

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

Issue - State: closed - Opened by FriederikeHanssen 6 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 6 months ago - 11 comments

#3080 - Fail to send the completion email

Issue - State: open - Opened by HaidYi 6 months ago
Labels: bug

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

Pull Request - State: closed - Opened by renovate[bot] 6 months ago

#3078 - Update gitpod/workspace-base Docker digest to f189a41

Pull Request - State: closed - Opened by renovate[bot] 6 months ago

#3077 - Add option `--fix` to update the `meta.yml` file of subworkflows.

Pull Request - State: closed - Opened by mirpedrol 6 months ago - 1 comment

#3076 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.0

Pull Request - State: closed - Opened by renovate[bot] 6 months ago

#3075 - lint fails missing variables that are present

Issue - State: closed - Opened by mandysulli 6 months ago - 6 comments
Labels: bug

#3073 - Fix 3068

Pull Request - State: closed - Opened by LaurenceKuhl 6 months ago - 1 comment

#3072 - Remove release announcement for non nf-core pipelines

Pull Request - State: closed - Opened by LaurenceKuhl 6 months ago

#3071 - Update python:3.12-slim Docker digest to f11725a

Pull Request - State: closed - Opened by renovate[bot] 6 months ago

#3069 - No nf-core modules found

Issue - State: closed - Opened by mandysulli 6 months ago - 8 comments
Labels: bug

#3068 - nf-core create fails on 2.14.2.dev0

Issue - State: closed - Opened by SPPearce 6 months ago - 1 comment
Labels: bug

#3067 - Allow numbers in pipeline names

Issue - State: open - Opened by adamrtalbot 6 months ago - 3 comments
Labels: enhancement

#3065 - Lint for pipeline nf-test contents

Issue - State: open - Opened by adamrtalbot 6 months ago
Labels: enhancement

#3064 - Lint for tests/nextflow.config contents

Issue - State: open - Opened by adamrtalbot 6 months ago
Labels: enhancement

#3063 - Lint contents of nf-test.config

Issue - State: open - Opened by adamrtalbot 6 months ago
Labels: enhancement

#3061 - handle new jsonschema error type

Pull Request - State: closed - Opened by mashehu 6 months ago

#3060 - Update dependency textual to v0.72.0

Pull Request - State: closed - Opened by renovate[bot] 6 months ago

#3059 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.4

Pull Request - State: closed - Opened by renovate[bot] 6 months ago - 2 comments

#3058 - Update to pytest v8 and move it to dev dependencies

Pull Request - State: closed - Opened by mashehu 6 months ago

#3057 - Lint unused import

Issue - State: open - Opened by LouisLeNezet 6 months ago
Labels: linting, enhancement

#3056 - modules test on a private modules server requires --git-remote

Issue - State: open - Opened by SPPearce 6 months ago
Labels: bug

#3055 - template: Use filename in code block for `params.yml`

Pull Request - State: closed - Opened by mashehu 6 months ago

#3054 - update api docs to new structure

Pull Request - State: closed - Opened by mashehu 6 months ago

#3053 - Action Required: Fix Renovate Configuration

Issue - State: closed - Opened by renovate[bot] 7 months ago

#3052 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1

Pull Request - State: closed - Opened by renovate[bot] 7 months ago

#3051 - update output_dir for api docs to new website structure

Pull Request - State: closed - Opened by mashehu 7 months ago

#3050 - Update python:3.12-slim Docker digest to d5f1674

Pull Request - State: closed - Opened by renovate[bot] 7 months ago

#3049 - linting for nf-test snapshot

Issue - State: open - Opened by maxulysse 7 months ago - 1 comment
Labels: enhancement

#3048 - Update gitpod/workspace-base Docker digest to 0f38224

Pull Request - State: closed - Opened by renovate[bot] 7 months ago - 1 comment

#3047 - add flagg limit_output for modules update

Pull Request - State: closed - Opened by Joon-Klaps 7 months ago - 4 comments

#3046 - Remove deprecated syntax

Pull Request - State: closed - Opened by maxulysse 7 months ago - 4 comments

#3045 - Add flag to limit diff output of modules update

Issue - State: closed - Opened by Joon-Klaps 7 months ago
Labels: enhancement

#3044 - Subworkflow install failure still results in a 0 exit code

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

#3043 - Non-CLI usage of nf-core download

Issue - State: closed - Opened by seedgeorge 7 months ago - 5 comments
Labels: awaiting-feedback, Stale, download

#3042 - Template: Run awsfulltest on PRs to `master` with two PR approvals

Pull Request - State: closed - Opened by mashehu 7 months ago - 1 comment

#3041 - Update python:3.12-slim Docker digest to da2d7af

Pull Request - State: closed - Opened by renovate[bot] 7 months ago - 1 comment

#3040 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.0

Pull Request - State: closed - Opened by renovate[bot] 7 months ago - 1 comment

#3039 - move pipeline commands to functions to avoid duplication

Pull Request - State: closed - Opened by mirpedrol 7 months ago

#3038 - Create app: display input textbox with equally spaced grid

Pull Request - State: closed - Opened by mirpedrol 7 months ago

#3037 - Replace check_max function with resourceLimits directive

Pull Request - State: closed - Opened by jfy133 7 months ago - 8 comments

#3036 - Add warning deprecation message to top-level commands

Pull Request - State: closed - Opened by mirpedrol 7 months ago

#3035 - Revert "move pipeline subcommands for v3.0"

Pull Request - State: closed - Opened by mirpedrol 7 months ago - 1 comment

#3034 - Download CI erroring since is using development version of tools

Issue - State: closed - Opened by JoseEspinosa 7 months ago - 1 comment
Labels: bug

#3033 - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.1

Pull Request - State: closed - Opened by renovate[bot] 7 months ago - 1 comment

#3032 - Modules meta.yml ontology

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

#3031 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10

Pull Request - State: closed - Opened by renovate[bot] 7 months ago

#3030 - `nf-core schema build` uses old schema in json file

Issue - State: closed - Opened by SimonDMurray 7 months ago - 2 comments
Labels: bug

#3029 - Linting: Remove 'defaults' from conda environment.yml file.

Pull Request - State: closed - Opened by ewels 7 months ago - 2 comments

#3028 - Module meta.yml restructure

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

#3027 - CLI helper to select EDAM ontologies for module inputs / outputs

Issue - State: open - Opened by ewels 7 months ago
Labels: command line tools, modules

#3026 - Fetch bio.tools identifiers for module YAML file

Issue - State: open - Opened by ewels 7 months ago
Labels: command line tools, modules

#3025 - pytest

Issue - State: closed - Opened by muffato 7 months ago - 1 comment

#3024 - Remove release announcement from non nf-core pipelines

Pull Request - State: closed - Opened by LaurenceKuhl 7 months ago - 1 comment

#3023 - Update python:3.12-slim Docker digest to 2fba8e7

Pull Request - State: closed - Opened by renovate[bot] 7 months ago

#3022 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.9

Pull Request - State: closed - Opened by renovate[bot] 7 months ago

#3021 - Lint for correct `meta.yml` tuple structure in modules and subworkflows

Issue - State: closed - Opened by mirpedrol 7 months ago
Labels: modules, enhancement

#3020 - Update python:3.12-slim Docker digest to e3ae8cf

Pull Request - State: closed - Opened by renovate[bot] 7 months ago

#3019 - Support NXF_SINGULARITY_LIBRARYDIR in `nf-core download`

Issue - State: open - Opened by muffato 8 months ago - 4 comments
Labels: enhancement, download

#3018 - ci: Run checks on renovate branches to avoid creating and merging PRs

Pull Request - State: open - Opened by edmundmiller 8 months ago - 1 comment

#3017 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8

Pull Request - State: closed - Opened by renovate[bot] 8 months ago

#3016 - Update dawidd6/action-download-artifact action to v6

Pull Request - State: closed - Opened by renovate[bot] 8 months ago

#3015 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7

Pull Request - State: closed - Opened by renovate[bot] 8 months ago

#3014 - Conda module linting: Include package name in log file

Pull Request - State: closed - Opened by ewels 8 months ago - 2 comments

#3013 - README - absolute image paths

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

#3012 - Remove nf-core licences command

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 1 comment

#3011 - meta information not matching between main.nf and meta.yml should result in failure

Issue - State: closed - Opened by mahesh-panchal 8 months ago - 1 comment
Labels: enhancement

#3009 - nf-core lint should say which conda packages are not specified correctly

Issue - State: closed - Opened by mahesh-panchal 8 months ago
Labels: enhancement

#3007 - Create: Mock git cretentials to generate stable textual snapshots

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 2 comments

#3006 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6

Pull Request - State: closed - Opened by renovate[bot] 8 months ago

#3005 - Add organization to `main.nf.test` tag instead of using `nfcore`

Pull Request - State: closed - Opened by nvnieuwk 8 months ago - 2 comments
Labels: template, modules, enhancement, subworkflows

#3004 - TEST self-hosted runers: DO NOT MERGE

Pull Request - State: closed - Opened by mirpedrol 8 months ago

#3003 - return directory if base_dir is the root directory

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 1 comment

#3002 - can't create nf-core.yml file

Issue - State: closed - Opened by paulsenlab 8 months ago - 4 comments
Labels: bug

#3001 - Add nf-core configs create sub command (attempt 2)

Pull Request - State: open - Opened by jfy133 8 months ago - 2 comments

#3000 - nf-core lint stack trace error list index out of range

Issue - State: closed - Opened by mahesh-panchal 8 months ago - 1 comment
Labels: bug

#2998 - update minimal textual version and snapshots

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 1 comment

#2997 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.5

Pull Request - State: closed - Opened by renovate[bot] 8 months ago

#2996 - Add native support for multiple `org_path` in modules and subworkflows directories

Issue - State: open - Opened by AlexVCaron 8 months ago - 3 comments
Labels: enhancement

#2995 - Removes tags.yml from module and subworkflow template

Pull Request - State: closed - Opened by adamrtalbot 8 months ago - 9 comments

#2994 - Add pipeline nf-test tests

Issue - State: open - Opened by mirpedrol 8 months ago
Labels: pipeline-testing, nf-test

#2993 - Lean down CLI for remote component repositories

Issue - State: open - Opened by AlexVCaron 8 months ago - 4 comments
Labels: command line tools

#2992 - Add pipeline level nf-tests for template

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

#2991 - Add no clobber and put bash options on their own line

Pull Request - State: closed - Opened by mahesh-panchal 8 months ago - 5 comments

#2990 - Update test after updating bwa/mem module

Pull Request - State: closed - Opened by mirpedrol 8 months ago

#2989 - Update release checklist

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 2 comments

#2988 - Update output of generation script for API docs to new structure

Pull Request - State: closed - Opened by mashehu 8 months ago