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Strip pinned node version in GitHub actions
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Also revert auto-markdown fixing in template markdown files.
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ewels committed Feb 8, 2022
1 parent e80474f commit 45172e2
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Showing 4 changed files with 7 additions and 15 deletions.
4 changes: 1 addition & 3 deletions .github/workflows/markdown-lint.yml
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Expand Up @@ -7,9 +7,7 @@ jobs:
steps:
- uses: actions/checkout@v2

- uses: actions/setup-node@v1
with:
node-version: "16"
- uses: actions/setup-node@v2

- name: Install markdownlint
run: npm install -g markdownlint-cli
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -8,7 +8,7 @@
* Replaced equals with ~ in nf-core headers, to stop false positive unresolved conflict errors when committing with VSCode.
* Add retry strategy for AWS megatests after releasing [nf-core/tower-action v2.2](https://github.com/nf-core/tower-action/releases/tag/v2.2)
* Update igenomes path to the `BWAIndex` to fetch the whole `version0.6.0` folder instead of only the `genome.fa` file
* Bump Node version to 16 in the GitHub Actions workflows, to fix errors with `markdownlint`
* Remove pinned Node version in the GitHub Actions workflows, to fix errors with `markdownlint`

## General

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12 changes: 3 additions & 9 deletions nf_core/pipeline-template/.github/workflows/linting.yml
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Expand Up @@ -12,9 +12,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: '16'
- uses: actions/setup-node@v2
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Run Markdownlint
Expand Down Expand Up @@ -51,9 +49,7 @@ jobs:
steps:
- uses: actions/checkout@v2

- uses: actions/setup-node@v1
with:
node-version: '16'
- uses: actions/setup-node@v2

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -65,9 +61,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v1
with:
node-version: '16'
- uses: actions/setup-node@v2
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
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4 changes: 2 additions & 2 deletions nf_core/pipeline-template/docs/usage.md
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@@ -1,6 +1,6 @@
# {{ name }}: Usage

## :warning: Please read this documentation on the nf-core website: [<https://nf-co.re/>{{ short_name }}/usage](<https://nf-co.re/>{{ short_name }}/usage)
## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/{{ short_name }}/usage](https://nf-co.re/{{ short_name }}/usage)

> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
Expand Down Expand Up @@ -83,7 +83,7 @@ nextflow pull {{ name }}

It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.

First, go to the [{{ name }} releases page](<https://github.com/>{{ name }}/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.
First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`.

This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.

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