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Prepare release 2.1.0 #96

Merged
merged 4 commits into from
Oct 23, 2023
Merged

Prepare release 2.1.0 #96

merged 4 commits into from
Oct 23, 2023

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Daniel-VM
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This prepare the dev branch for release 2.1.0.
Following PR will merge this release from dev into master .

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Oct 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 84b58ac

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-23 09:19:07

d4straub
d4straub approved these changes Oct 20, 2023
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LGTM

@d4straub
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d4straub commented Oct 20, 2023 •
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But actually, looking at https://nf-co.re/bacass/dev, some small stuff isnt rendered perfectly.
E.g.:

  • "usage": link in An [example samplesheet](https://nf-co.re/bacass/dev/assets/samplesheet.tsv) has been provided with the pipeline. broken?
  • "introduction": block below Default: Short read assembly with Unicycler, --kraken2db can be any compressed database (.tar.gz/.tgz): seems broken

@d4straub
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The test warnings complains about some TODO strings, those could be deleted if not relevant any more.

@Daniel-VM
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But actually, looking at https://nf-co.re/bacass/dev, some small stuff isnt rendered perfectly. E.g.:

* "usage": link in `An [example samplesheet](https://nf-co.re/bacass/dev/assets/samplesheet.tsv) has been provided with the pipeline.` broken?

Strange... I think the link in the markdown is correct: [example samplesheet](../assets/samplesheet.tsv).

* "introduction": `block below Default: Short read assembly with Unicycler, --kraken2db can be any compressed database (.tar.gz/.tgz):` seems broken

I can access the link without any issue in my case

@Daniel-VM
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Do you know if there is any method to debug the rendering process? (files to check, tools to use etc.)

@d4straub
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Do you know if there is any method to debug the rendering process? (files to check, tools to use etc.)

unfortunately not. I attempt to learn from examples and then test by adding a PR :D

@Daniel-VM
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But actually, looking at https://nf-co.re/bacass/dev, some small stuff isnt rendered perfectly. E.g.:

* "usage": link in `An [example samplesheet](https://nf-co.re/bacass/dev/assets/samplesheet.tsv) has been provided with the pipeline.` broken?

I am not completely sure, but I think that this link, which is created with the nf-core templates (I assume), will always be broken. After checking this line in several pipelines, I noticed that all of them end up with the same issue.

It seems to me that this line is intended to be a markdown link only, but not a URL.

@Daniel-VM
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Daniel-VM commented Oct 22, 2023 •
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Yes, the link is broken and I found an issue related: nf-core/website-issue#2045.

We could replace the line and proceed with the merge, or just proceed with the merge. Awaiting your approval ;) 👍🏾

@d4straub
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Hi, sorry for the late reply.

About the link to the samplesheet: Ok then ignore it, good that there is an issue already.

About:

* "introduction": `block below Default: Short read assembly with Unicycler, --kraken2db can be any compressed database (.tar.gz/.tgz):` seems broken

I can access the link without any issue in my case

I meant the part below, see the screenshot
image

But that are small problems, you can go ahead with merging I think.

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Got it! I have pushed changes to have the release version as clean as possible. 👍🏾

@Daniel-VM Daniel-VM merged commit 3f6d59b into nf-core:dev Oct 23, 2023
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