nf-core/tools issues and pull requests

#2775 - fix generate api docs script, gsed-> sed [skip changelog]

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

#2774 - Have module_changes.py check main.test.nf and environment.yml

Issue - State: open - Opened by asp8200 7 months ago
Labels: enhancement

#2773 - fix api docs build request (next attempt) [skip changelog]

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

#2772 - fix github action syntax, remove now unneeded makefile [skip changelog]

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

#2771 - Modules: patch: handle file not found when it is an added file to a module

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

#2770 - Modules: Handle symlinks when migrating pytest

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

#2769 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.2

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment

#2768 - nf-core download: Create container image symlinks so images are still found, even if registry config diverges.

Pull Request - State: closed - Opened by MatthiasZepper 8 months ago - 1 comment
Labels: high-priority, download

#2767 - Modules: Add `--profile` parameter to nf-test command

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

#2766 - Update actions/github-script action to v7

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

#2765 - chore(deps): update dawidd6/action-download-artifact digest to f6b0bac - abandoned

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2764 - Pin actions/github-script action to d7906e4 - autoclosed

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

#2763 - Modules: keep custom *.config files also after `nf-core modules/subworkflows update`

Pull Request - State: closed - Opened by mashehu 8 months ago - 3 comments

#2762 - Linting: Handle multiple aliases in module imports correctly during linting

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

#2761 - template: add hashtags to release announcement on mastodon

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

#2760 - Update release social media auto-posting to include hashtags

Issue - State: closed - Opened by jfy133 8 months ago - 1 comment
Labels: enhancement

#2759 - nf-core modules and subworkflows commands should be case insensitive

Issue - State: closed - Opened by adamrtalbot 8 months ago - 1 comment
Labels: command line tools, good-first-issue

#2758 - Switch to markdown based API and linting error docs

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

#2757 - Template: Fix GitHub Actions CI and Linting badges links

Pull Request - State: closed - Opened by RaqManzano 8 months ago - 1 comment
Labels: linting

#2756 - chore(deps): pin jlumbroso/free-disk-space action to 54081f1

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment

#2755 - Add Github Action to automatically cleanup ubuntu-latest runners to fix runner running out of diskspace errors

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

#2754 - Github Action Runners run out of diskspace

Issue - State: closed - Opened by apeltzer 8 months ago - 2 comments
Labels: bug

#2753 - Add --profile flag to `nf-core modules test` to allow CLI speification of container/conda engine

Issue - State: closed - Opened by jfy133 8 months ago - 1 comment
Labels: enhancement

#2752 - Update python:3.11-slim Docker digest to ce81dc5

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment

#2751 - nf-core download has wrong name for singularity converted containers

Issue - State: closed - Opened by maxulysse 8 months ago - 6 comments
Labels: bug, download

#2750 - Fix some docstrings [skip changelog]

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

#2749 - Module update fails if there is a new file (even if module is patched)

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

#2748 - Schema: Write future reference schema

Issue - State: open - Opened by ewels 8 months ago - 1 comment
Labels: schema

#2747 - Update gitpod/workspace-base Docker digest to 45e7617

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment

#2746 - nf-core lint fails when there are no external modules

Issue - State: closed - Opened by sgopalan98 8 months ago - 1 comment
Labels: bug, high-priority

#2745 - Update nf-core/setup-nextflow digest to b9f764e

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

#2744 - linting: add looser comparison when linting pipeline logos

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

#2743 - Update python:3.11-slim Docker digest to 2a746e2

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2742 - Template: fix jinja rendering of download_pipeline.yml

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

#2741 - Add the template version to the pipeline `.nf-core.yml` file

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

#2740 - only paths or paths-ignore is allowed for actions [skip changelog]

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

#2739 - Update actions/setup-python action to v5

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

#2738 - Update actions/checkout action to v4

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

#2737 - Pin dependencies

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

#2736 - Remove lib directory and replace it with granular utils_* subworkflows

Pull Request - State: closed - Opened by drpatelh 8 months ago - 3 comments

#2735 - Changelog bot should add reviewers

Issue - State: open - Opened by mashehu 8 months ago - 2 comments
Labels: automation

#2734 - Handle dirty local module repos by force checkout of commits and branches if needed

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

#2733 - make creat-lint-wf composable and regularly update components in template

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

#2732 - Add `--target` parameter to `nf-core modules|subworkflows install`

Issue - State: open - Opened by mashehu 8 months ago
Labels: command line tools, enhancement

#2731 - New functionality: `nf-core config create`

Issue - State: open - Opened by jfy133 8 months ago - 1 comment
Labels: enhancement

#2730 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1

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

#2729 - Update README.md

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

#2728 - Update codecov/codecov-action digest to e0b68c6

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 1 comment

#2727 - Pipeline template: Fix download test CI

Pull Request - State: closed - Opened by MatthiasZepper 8 months ago - 4 comments
Labels: bug, download

#2726 - Linting with nf-core tools 2.12.1 throws a warning when using multiple alias imports

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

#2725 - update ruff to 0.2.0 and add it to pre-commit step

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

#2724 - update ruff for dev tools [skip changelog]

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

#2723 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.0

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2722 - fix ignoring changes in partial template files

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

#2721 - bump version to 2.13dev

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

#2720 - Pin dependencies

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

#2719 - Revert pin dependency

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

#2718 - Dev -> Master for 2.12.1

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

#2717 - Bump version to 2.12.1

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

#2716 - Ignore nf-core-bot in renovate PRs

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

#2715 - Update nf-core/setup-nextflow digest to dccbf84 - abandoned

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2714 - Update codecov/codecov-action digest to ab904c4

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2713 - Update codecov/codecov-action action to v4

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2712 - use types for default value comparison

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

#2711 - handle float values correctly in default value comparison

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

#2710 - Linting and formatting of exponent values do not agree with each other in pipeline nextflow schema vs json

Issue - State: closed - Opened by jfy133 8 months ago - 2 comments
Labels: bug

#2709 - Print relative path not absolute path in logo cmd log output

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

#2708 - fix changelog titles

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

#2707 - Linting: fix ignoring files_unchanged

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 3 comments

#2706 - Avoid conflicts between editorconfig and prettier linting

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

#2705 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2704 - nf-core lint failing for mismatching assets/sendmail_template.txt

Issue - State: open - Opened by drpatelh 8 months ago
Labels: bug

#2703 - Linting: Handle default values of type number from nextflow schema

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

#2702 - bump to 2.13dev [skip changelog]

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

#2701 - Pin dependencies

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2700 - Fix logo links [skip changelog]

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

#2699 - add documentation for create-logo command [no changelog]

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

#2698 - dev -> master for 2.12

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

#2697 - use correct prettier version in pre-commit template [no changelog]

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

#2696 - bump to 2.12 for release [skip changelog]

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

#2695 - Update peter-evans/create-or-update-comment action to v4

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

#2694 - Nicer lint bot comment again

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

#2693 - Revert "template: add 👀👍🏻🎉😕 reactions to fix-linting bot action"

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

#2692 - template: add 👀👍🏻🎉😕 reactions to fix-linting bot action

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

#2691 - Test new linting comment [no changelog]

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

#2690 - debug fix-linting comment [no changelog]

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

#2689 - Linting: fix bug when linting subworkflows from pipeline lint [skip changelog]

Pull Request - State: closed - Opened by mirpedrol 8 months ago - 3 comments

#2688 - Add new error message pointing to docs when 'requirement exceeds available memory' error message

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

#2687 - reviewdog integration

Issue - State: open - Opened by edmundmiller 8 months ago
Labels: enhancement

#2686 - Linting: allow ignoring specific files when linting template_strings

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

#2685 - test using xdist for faster tests [skip changelog]

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

#2684 - Linting: lint `nextflow.config` default values match the ones specified in `nextflow_schema.json`

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

#2683 - Update peter-evans/create-or-update-comment action to v4

Pull Request - State: closed - Opened by renovate[bot] 8 months ago - 2 comments

#2682 - modules pytest migration flag fails to remove symlinked pytest directories

Issue - State: closed - Opened by jfy133 8 months ago - 1 comment
Labels: bug

#2681 - fix-linting comments both on failure and success

Issue - State: closed - Opened by mashehu 8 months ago
Labels: bug

#2680 - Add new command `nf-core rocrate` to create a Research Object (RO) crate for a pipeline

Pull Request - State: open - Opened by mashehu 8 months ago - 15 comments

#2679 - Add new command `nf-core rocrate` to create a Research Object crate for a pipeline

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

#2678 - Template: add function to check `-profile` is well formatted

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

#2677 - Linting: linting a pipeline also lints the installed subworkflows

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

#2676 - Linting: environment.yml name must be lowercase

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

GitHub / nf-core/tools issues and pull requests