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RC 3.16.0 #1395

Merged
merged 121 commits into from
Oct 2, 2024
Merged

RC 3.16.0 #1395

merged 121 commits into from
Oct 2, 2024

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maxulysse
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@maxulysse maxulysse commented Sep 30, 2024

Release Candidate 3.16.0 aka Fire Ferret

Merge only once #1394 is merged

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!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • 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 Sep 30, 2024

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 00a0857

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.16.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-02 12:25:51

@maxulysse maxulysse changed the title RC 3.15.2 RC 3.16.0 Oct 1, 2024
@MatthiasZepper
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What do we do with #1369 ?

@siddharthab made such an awesome effort, and it is essentially done - the tool is just horribly slow on transcriptomic alignments, so we are since weeks waiting that the tool's author will merge a tiny PR that fixes that. I am seriously considering forking the repo and merge it there...because I so badly want that tool in the pipeline.

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Only thing I would say I'm unhappy with is the extremely minimal description of the input file for --kraken2_db.

A kraken2 database is not the same as a bracken database (bracken requires multiple extra files alongside the normal kraken2 database files), and the Ben Langmead things I guess is being assumed is the ones most people use are not actually really the gold standard (there aren't any).

I would suggest improving the description of what gets supplied to that paramneter (a tar.gz) and also in usage explain further what is accepted and when depending on if you're supplying kraken vs bracken parameters.

But otherwise everything else is self-explanatory (thus the approval)

| `Bracken` | ----------- | 2.9 |

> **NB:** Dependency has been **updated** if both old and new version information is present.
>
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Suggested change
>

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I like the line breaks here

> **NB:** Dependency has been **updated** if both old and new version information is present.
>
> **NB:** Dependency has been **added** if just the new version information is present.
>
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Suggested change
>

},
"kraken_db": {
"type": "string",
"description": "Database when using Kraken2/Bracken for contaminant screening.",
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In what form? Should this be a directory or a tar.gz file?

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OR both? The Ben Langmead versions are tar.gz for example

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@egreenberg7 any idea about that?

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I'll make sure to include the answer to that when we make tests for this new feature in the next release

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Should be a tar.gz file since the nf-core Kraken2 and Bracken modules use the --gzip-compressed option. It probably should be clarified that kraken2 and bracken databases are distinct, but they are often zipped together (as in the pre-built indices). A separate --bracken_db option potentially could be added.

While the pre-built files are not gold standard, they provide a quick/convenient option for people who want to run contamination detection without getting into the weeds of the tools. I'll note that I did not offer the ability to make a standard database in an indexing run of the pipeline because it is so much slower than just downloading pre-built indices (and rather computationally expensive).

In any case, @jfy133 has much more experience than me with metagenomics tools, so I would defer to any changes he recommends to either the Usage tab or the input

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf Outdated Show resolved Hide resolved
//Check that Kraken/Bracken parameters are not provided when Kraken2 is not being used
} else {
if (!params.bracken_precision.equals('S')) {
brackenPrecisionWithoutKrakenDBWarn()
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Is a function here really necessary? You only use it once...

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Good spot, that'll be looked after in some slight refactoring, but out of scope for this release

tests/default.nf.test Show resolved Hide resolved
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@maxulysse
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What do we do with #1369 ?

@siddharthab made such an awesome effort, and it is essentially done - the tool is just horribly slow on transcriptomic alignments, so we are since weeks waiting that the tool's author will merge a tiny PR that fixes that. I am seriously considering forking the repo and merge it there...because I so badly want that tool in the pipeline.

This was intended to be just a patch release, Kraken2/Bracken was already in so we release as 3.16.0, but it was really meant to be 3.15.2

#1369 will be included in the next release

Co-authored-by: James A. Fellows Yates <[email protected]>
@MatthiasZepper
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What do we do with #1369 ?
@siddharthab made such an awesome effort, and it is essentially done - the tool is just horribly slow on transcriptomic alignments, so we are since weeks waiting that the tool's author will merge a tiny PR that fixes that. I am seriously considering forking the repo and merge it there...because I so badly want that tool in the pipeline.

This was intended to be just a patch release, Kraken2/Bracken was already in so we release as 3.16.0, but it was really meant to be 3.15.2

#1369 will be included in the next release

Fine with me.

BTW: You are not very patriotic, are you? Why would you chose "Fire" as an element, if you could have chosen Francium and honor your home country 😉

@maxulysse
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What do we do with #1369 ?
@siddharthab made such an awesome effort, and it is essentially done - the tool is just horribly slow on transcriptomic alignments, so we are since weeks waiting that the tool's author will merge a tiny PR that fixes that. I am seriously considering forking the repo and merge it there...because I so badly want that tool in the pipeline.

This was intended to be just a patch release, Kraken2/Bracken was already in so we release as 3.16.0, but it was really meant to be 3.15.2
#1369 will be included in the next release

Fine with me.

BTW: You are not very patriotic, are you? Why would you chose "Fire" as an element, if you could have chosen Francium and honor your home country 😉

https://avatar.fandom.com/wiki/Fire_ferret

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Weeee

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Wow, so much ignored!

@maxulysse maxulysse merged commit 33df0c0 into master Oct 2, 2024
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9 participants