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WIP Internal Benchmarking#1721

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famosab wants to merge8 commits intonf-core:dev
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WIP Internal Benchmarking#1721

famosab wants to merge8 commits intonf-core:devfromfamosab:bench

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@famosab
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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 thecontribution docs
  • If necessary, also make a PR on the nf-core/sarekbranch on thenf-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 indocs/usage.md is updated.
  • Output Documentation indocs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

This continues#1448

@famosabfamosab mentioned this pull requestNov 1, 2024
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@famosab
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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-actionsbot commentedNov 1, 2024•
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nf-core pipelines lint overall result: Passed ✅⚠️

Posted for pipeline commit77e713a

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

❗ Test warnings:

  • pipeline_todos - TODO string inmain.nf:Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string inmain.nf:Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string inmain.nf:Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string inbase.config:Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at2024-11-01 17:31:34

@maxulysse
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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?

@famosab
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@maxulysse both 24.10

@asp8200
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@maxulysse both 24.10

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

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

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@FriederikeHanssenFriederikeHanssenAwaiting requested review from FriederikeHanssenFriederikeHanssen will be requested when the pull request is marked ready for reviewFriederikeHanssen is a code owner

@maxulyssemaxulysseAwaiting requested review from maxulyssemaxulysse will be requested when the pull request is marked ready for reviewmaxulysse is a code owner

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@famosab@maxulysse@asp8200
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