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WIP Internal Benchmarking#1721

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nf-core:devfrom
famosab:bench
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WIP Internal Benchmarking#1721
famosab wants to merge 8 commits into
nf-core:devfrom
famosab:bench

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@famosab
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@famosab famosab commented Nov 1, 2024

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/sarek 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).

This continues #1448

@famosab famosab mentioned this pull request Nov 1, 2024
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@famosab
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famosab commented Nov 1, 2024

This currently runs with

nextflow run main.nf -profile docker -c conf/benchmark.config --outdir '../test-sarek-bench'

On my local computer it starts running but when I take it to our linux workstation I always get

Missing process or function Channel.empty([[]])

 -- Check script 'main.nf' at line: 343 or see '.nextflow.log' file for more details

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github-actions Bot commented Nov 1, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 77e713a

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-01 17:31:34

@maxulysse
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maxulysse commented Nov 1, 2024

This currently runs with

nextflow run main.nf -profile docker -c conf/benchmark.config --outdir '../test-sarek-bench'

On my local computer it starts running but when I take it to our linux workstation I always get

Missing process or function Channel.empty([[]])

 -- Check script 'main.nf' at line: 343 or see '.nextflow.log' file for more details

Which Nextflow version?

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famosab commented Nov 4, 2024

@maxulysse both 24.10

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asp8200 commented Nov 6, 2024

@maxulysse both 24.10

The issue with Missing process or function Channel.empty([[]]) will perhaps be solved with #1624

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famosab commented Nov 6, 2024

It ran when reverting to 24.04
Somehow the process RTGTOOLS_VCFEVAL was not triggered, RTGTOOLS_FORMAT ran as expected and produced the desired output.

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famosab commented Mar 12, 2025

I will get back to this PR in a couple of weeks :)

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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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@famosab @maxulysse @asp8200