Important! Template update for nf-core/tools v3.1.0 #1747
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nf-core-bot
requested review from
FriederikeHanssen and
maxulysse
as code owners
| - streetsidesoftware.code-spell-checker # Spelling checker for source code | ||
| - charliermarsh.ruff # Code linter Ruff | ||
| extensions: | ||
| #- nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack |
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A fix for this is added to the template now
| #- nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack | |
| - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack |
| "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164", | ||
| "installed_by": ["modules"] | ||
| }, | ||
| "fgbio/callmolecularconsensusreads": { |
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were these modules not in modules.conig before? 🤔
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yes, but not from the template
| // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 | ||
| [ | ||
| name: 'Maxime Garcia', | ||
| affiliation: '', |
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the information for each author should be updated manually
| prov { | ||
| enabled = true | ||
| formats { | ||
| bco { | ||
| file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json" | ||
| } | ||
| } | ||
| } |
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sorry, I think I added this by mistake when resolving merge conflicts
| prov { | |
| enabled = true | |
| formats { | |
| bco { | |
| file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json" | |
| } | |
| } | |
| } |
| @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). | |||
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| Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. | |||
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| Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) | |||
| Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/main/.github/CONTRIBUTING.md) | |||
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So if we only mention main here, we have to switch all over the place, no?
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this is now master because the default branch was master, once you change defaultBranch from the manifest and run nf-core pipelines sync all of these mentions will change to main.
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actually, sorry, this was not true, the default branch is automatically detected from the git configuration :)
| @@ -1,6 +1,6 @@ | |||
| { | |||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | |||
| "$id": "https://raw.githubusercontent.com/nf-core/sarek/master/assets/schema_input.json", | |||
| "$id": "https://raw.githubusercontent.com/nf-core/sarek/main/assets/schema_input.json", | |||
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So if we only mention main here, we have to switch all over the place, no?
| homePage = 'https://github.com/nf-core/sarek' | ||
| description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" | ||
| mainScript = 'main.nf' | ||
| defaultBranch = 'main' |
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ok, so we really have to switch to main
| @@ -421,7 +456,7 @@ validation { | |||
| https://doi.org/10.1038/s41587-020-0439-x | |||
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| * Software dependencies | |||
| https://github.com/${manifest.name}/blob/master/CITATIONS.md | |||
| https://github.com/nf-core/sarek/blob/master/CITATIONS.md | |||
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| https://github.com/nf-core/sarek/blob/master/CITATIONS.md | |
| https://github.com/nf-core/sarek/blob/main/CITATIONS.md |
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@mirpedrol this one is still master
| - On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. | ||
| - Fix the bug, and bump version (X.Y.Z+1). | ||
| - A PR should be made on `master` from patch to directly this particular bug. | ||
| - Open a pull-request from `patch` to `main`/`master` with the changes. |
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@mirpedrol ok, so I don't think we need to mention master here if we move all to main in all other locations already
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closing this one, so we can open a new test PR |
Version
3.1.0of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.1.0branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v3.1.0release page.