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Remove universc subworkflow from pipeline #396

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Remove universc subworkflow from pipeline #396

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@fmalmeida fmalmeida commented Dec 3, 2024 •
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Opening a PR to address #289 . Decision was made to remove universc from pipeline since it was broke for quite a while and there was no request for fixing it during period.

PR checklist

  • 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).

zxBIB Almeida,Felipe (GCBDS) EXTERNAL added 2 commits December 3, 2024 08:59
@fmalmeida fmalmeida requested a review from grst December 3, 2024 08:10
@fmalmeida fmalmeida self-assigned this Dec 3, 2024
@fmalmeida fmalmeida linked an issue Dec 3, 2024 that may be closed by this pull request
Update or remove universc #289
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@fmalmeida
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Hi @grst ,
If I understand correctly, the work on #289 would be addressed by what it is in this PR.

There is one thing though, we need to remove the universc information from the metromap.

Do you know who has created the metromap, or, are you able to quickly modify it?

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github-actions bot commented Dec 3, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5aa3068

+| ✅ 215 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-04 09:10:34

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grst commented Dec 3, 2024

Well the SVG is here: https://github.com/nf-core/scrnaseq/blob/master/docs/images/rnaseq_pipeline_V1.0-metro_clean.svg

@fmalmeida
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Hi @grst ,
Upon checking, it seems we already have a PNG without universc, but maybe was never migrated to use it:

https://github.com/nf-core/scrnaseq/blob/289-update-or-remove-universc/docs/images/scrnaseq_pipeline_v2.0_metro_clean.png

Probably we should just update the documentation to use it since it has the other included workflows.

One problem is that it does not have an SVG included.

Another point is, should the v1-0 files be removed?

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fmalmeida commented Dec 3, 2024 •
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Actually, now looking at it, it seems some changes in this v2-0 were never integrated.

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grst commented Dec 3, 2024

like, scATAC?

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Hi @grst ,
Do you think these are good enough for the release, but then we have to create an issue to try to properly address it in the next hackathon?

scrnaseq_pipeline_v1 0_metro_clean
srnaseq_pipeline_V3 0-metro_clean

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grst commented Dec 3, 2024

that's fine with me!

@fmalmeida fmalmeida marked this pull request as ready for review December 3, 2024 11:52
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Should then be ready for review, @grst

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Some tests are failing, other than that LGTM!

@fmalmeida
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Some tests are failing, other than that LGTM!

not sure why they failed, as there was no change to the processings :/

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Some tests are failing, other than that LGTM!

Hi @grst ,
The error on the tests are the java version. Do you know where we can change it?

Run nf-core/setup-nextflow@v2
Input version 'latest-everything' resolved to Nextflow v24.11.0-edge
Downloaded `nextflow` to /opt/hostedtoolcache/nextflow/24.11.0-edge/x64 and added to PATH
(node:83297) [DEP0147] DeprecationWarning: In future versions of Node.js, fs.rmdir(path, { recursive: true }) will be removed. Use fs.rm(path, { recursive: true }) instead
(Use `node --trace-deprecation ...` to show where the warning was created)
/opt/hostedtoolcache/nextflow/24.11.0-edge/x64/nextflow help
ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 17 or later (up to [23](https://github.com/nf-core/scrnaseq/actions/runs/12139073488/job/33853897755?pr=396#step:6:24)) is installed
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
 JAVA_CMD: /usr/lib/jvm/temurin-11-jdk-amd64/bin/java
 JAVA_HOME: /usr/lib/jvm/temurin-11-jdk-amd64

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grst commented Dec 4, 2024

See https://nfcore.slack.com/archives/CE6SDBX2A/p1733269671253319

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Update or remove universc
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