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[WIP] Benchmarking per pipeline / POC#1448

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famosab wants to merge 4 commits into
nf-core:devfrom
famosab:internal-bm
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[WIP] Benchmarking per pipeline / POC#1448
famosab wants to merge 4 commits into
nf-core:devfrom
famosab:internal-bm

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@famosab famosab commented Mar 22, 2024

This PR collects everything needed to add automated benchmarking to sarek.

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>).
  • 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).

@famosab famosab self-assigned this Mar 22, 2024
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github-actions Bot commented Mar 22, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 68bfaf7

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • schema_params - Param benchmark from nextflow config not found in nextflow_schema.json

❗ 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 WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-22 14:19:42

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famosab commented Aug 28, 2024 •
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It would make sense to move some of the subworkflows from the variantbenchmarking pipeline to the modules repo and re-use them in the banchmarking portion here.

Maybe starting this with small variants from germline calls: https://github.com/nf-core/variantbenchmarking/blob/dev/subworkflows/local/small_germline_benchmark.nf

@famosab famosab force-pushed the internal-bm branch 3 times, most recently from d50a88e to e8a60fe Compare August 30, 2024 15:04
@famosab famosab mentioned this pull request Nov 1, 2024
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famosab commented Nov 1, 2024

Continued in #1721

@famosab famosab closed this Nov 1, 2024
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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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