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Template update for nf-core/tools v4.2.1 #224
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0ab3233
Template update for nf-core/tools version 4.2.1
ljwharbers 4a5ee9c
Merge nf-core/tools 4.2.1 template into dev
ljwharbers 7c6e9fe
Refresh stale extended-test snapshots
ljwharbers c8db013
Fill in PR number in CHANGELOG entry
ljwharbers ed1ddae
Point manifest.diagram at the README metro map
ljwharbers bd5dace
CLAIR3: decide GPU mode from params.use_gpu
ljwharbers f1066e4
CLAIR3: GPU image v2.0.2_gpu -> v2.0.5_gpu
ljwharbers 0c1cf3f
Document --use_gpu: every affected tool and the Clair3 GPU limit
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| name: Fix linting from a comment | ||
| on: | ||
| issue_comment: | ||
| types: [created] # Add "@nf-core-bot fix linting" as a PR comment to trigger this workflow. | ||
|
|
||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.issue.number }} | ||
|
|
||
| jobs: | ||
| fix-linting: | ||
| uses: nf-core/actions/.github/workflows/fix-linting.yml@v1 | ||
| with: | ||
| nextflow-versions: '["25.10.4","latest-everything"]' | ||
| permissions: | ||
| actions: read | ||
| contents: read | ||
| issues: write | ||
| pull-requests: write | ||
|
|
||
| secrets: | ||
| BOT_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| { | ||
| // See https://github.com/nf-core/vscode-extensionpack | ||
| "recommendations": [ | ||
| "codezombiech.gitignore", | ||
| "esbenp.prettier-vscode", | ||
| "jebbs.markdown-extended", | ||
| "mechatroner.rainbow-csv", | ||
| "nextflow.nextflow", | ||
| "onnovalkering.vscode-singularity", | ||
| "redhat.vscode-yaml" | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| { | ||
| "markdown.styles": ["public/vscode_markdown.css"] | ||
| // Render nf-core website admonitions nicely in markdown previews | ||
| "markdown.styles": ["https://nf-co.re/vscode_markdown.css"] | ||
| } |
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This calls a reusable workflow by the mutable tag
@v1and passes itBOT_TOKEN(nf_core_bot_auth_token), a token that can push. The oldfix_linting.ymlpinned every action by SHA and also had agithub.repository == 'IntGenomicsLab/lrsomatic'guard, which is gone here.The same PR also unpins
nf-core/setup-nextflow@v3andnf-core/setup-nf-test@v2from SHAs to tags. That happens in.github/actions/nf-test/action.yml,.github/actions/get-shards/action.yml,linting.ymlanddownload_pipeline.yml, while every other action stays SHA-pinned. The PR description calls these changes "pin bumps".If unpinning the nf-core-owned actions is intended, please say so in the PR. Otherwise, pin them (and this reusable workflow) to commit SHAs with a
# vXcomment, as the rest of the workflows do.There was a problem hiding this comment.
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Kept as is on purpose. These lines are exactly what the nf-core/tools 4.2.1 template ships (
origin/TEMPLATEhasnf-core/setup-nextflow@v3,nf-core/setup-nf-test@v2andfix-linting.yml@v1). Re-pinning them here would make every future template sync conflict on these lines. Third-party actions stay SHA-pinned, as in the template.On the token:
nf_core_bot_auth_tokensecret (onlyCLAUDE_CODE_OAUTH_TOKENis set), soBOT_TOKENresolves to an empty string. Nothing with push rights is passed to the reusable workflow.nf-core/actionsfix-linting.yml@v1only runs on PR comments that contain@nf-core-bot fix linting, and it checks that the commenter has repository permission before doing anything.issue_commentworkflows from a fork run in the fork's own context, so the droppedgithub.repositoryguard didn't protect anything here.You're right that "pin bumps" in the PR description was misleading. I've corrected it to say the nf-core-owned actions now follow the template's tags.