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Merge pull request nf-core#2811 from nf-core/dev
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Dev -> Master for 2.13.1
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mashehu authored Feb 29, 2024
2 parents b51c7d8 + d6b459c commit 9eac5e9
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Showing 72 changed files with 2,404 additions and 2,036 deletions.
10 changes: 1 addition & 9 deletions .devcontainer/devcontainer.json
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Expand Up @@ -11,15 +11,7 @@
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},

// Add the IDs of extensions you want installed when the container is created.
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2 changes: 1 addition & 1 deletion .github/RELEASE_CHECKLIST.md
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Expand Up @@ -3,7 +3,7 @@
1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
4. Check that modules/subworkflows in tempalte are up to date with the latest releases
4. Check that modules/subworkflows in template are up to date with the latest releases
5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
6. Make sure all CI tests are passing!
7. Create a PR from `dev` to `master`
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2 changes: 1 addition & 1 deletion .github/actions/create-lint-wf/action.yml
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Expand Up @@ -17,7 +17,7 @@ runs:
# Set up Nextflow
- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1
with:
version: ${{ matrix.NXF_VER }}

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2 changes: 2 additions & 0 deletions .github/workflows/changelog.yml
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Expand Up @@ -4,6 +4,8 @@ on:
types: [created]
pull_request_target:
types: [opened]
branches:
- dev

jobs:
update_changelog:
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2 changes: 1 addition & 1 deletion .github/workflows/create-test-lint-wf-template.yml
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Expand Up @@ -72,7 +72,7 @@ jobs:
pip install .
- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1
with:
version: latest-everything

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2 changes: 1 addition & 1 deletion .github/workflows/create-test-wf.yml
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Expand Up @@ -59,7 +59,7 @@ jobs:
pip install .
- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1
with:
version: ${{ matrix.NXF_VER }}

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12 changes: 9 additions & 3 deletions .github/workflows/pytest.yml
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Expand Up @@ -108,12 +108,18 @@ jobs:
sudo add-apt-repository --remove ppa:git-core/ppa
sudo apt install -y git
- name: Set up Singularity
if: ${{ matrix.test == 'test_download.py'}}
uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
singularity-version: 3.8.3

- name: Get current date
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV

- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1

- name: Look if nf-test is already installed and write to env variable
id: check-nftest
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mv .github/.coveragerc .
- name: Download all artifacts
uses: actions/download-artifact@eaceaf801fd36c7dee90939fad912460b18a1ffe # v4
uses: actions/download-artifact@87c55149d96e628cc2ef7e6fc2aab372015aec85 # v4
- name: Run coverage
run: |
coverage combine --keep coverage*/.coverage*
coverage report
coverage xml
- uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044 # v4
- uses: codecov/codecov-action@54bcd8715eee62d40e33596ef5e8f0f48dbbccab # v4
with:
files: coverage.xml
env:
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2 changes: 1 addition & 1 deletion .github/workflows/rich-codex.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
cache-dependency-path: setup.py

- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1

- name: Cache nf-test installation
id: cache-software
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2 changes: 1 addition & 1 deletion .github/workflows/sync.yml
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Expand Up @@ -67,7 +67,7 @@ jobs:
pip install .
- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1
with:
version: "latest-everything"

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3 changes: 0 additions & 3 deletions .gitpod.yml
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Expand Up @@ -12,10 +12,7 @@ tasks:
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
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23 changes: 23 additions & 0 deletions CHANGELOG.md
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@@ -1,5 +1,28 @@
# nf-core/tools: Changelog

## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

### Template

- Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([#2795](https://github.com/nf-core/tools/pull/2795))
- Add nf-test test instructions to contributing and PR template ([#2807](https://github.com/nf-core/tools/pull/2807))
- Fix topic extraction step for hashtags in toots ([#2810](https://github.com/nf-core/tools/pull/2810))
- Update modules and subworkflows in the template ([#2811](https://github.com/nf-core/tools/pull/2811))
- Unpin setup-nextflow and action-tower-launch ([#2806](https://github.com/nf-core/tools/pull/2806))

### Download

- Improved offline container image resolution by introducing symlinks, fixes issues [#2751](https://github.com/nf-core/tools/issues/2751), [#2644](https://github.com/nf-core/tools/issues/2644) and [demultiplex#164](https://github.com/nf-core/demultiplex/issues/164): ([#2768](https://github.com/nf-core/tools/pull/2768))

### Linting

### Components

### General

- chore(deps): update codecov/codecov-action digest to 0cfda1d ([#2794](https://github.com/nf-core/tools/pull/2794))
- chore(deps): update gitpod/workspace-base docker digest to c15ee2f ([#2799](https://github.com/nf-core/tools/pull/2799))

## [v2.13 - Tin Puppy](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-20]

### Template
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