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Replacing local module BUILD_INTERVALS with nf-core mdule GAWK #1439

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merged 4 commits into from
Apr 3, 2024
Merged

Replacing local module BUILD_INTERVALS with nf-core mdule GAWK #1439

merged 4 commits into from
Apr 3, 2024

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asp8200
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@asp8200 asp8200 commented Mar 18, 2024 •
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Related to nf-core/modules#5132 (comment)

If approved, then similar a change should be done in the raredisease-pipeline.

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).

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github-actions bot commented Mar 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2edcdb1

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ 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 2024-03-18 16:30:57

@asp8200 asp8200 mentioned this pull request Mar 18, 2024
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maxulysse
maxulysse previously approved these changes Mar 18, 2024
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@asp8200 asp8200 marked this pull request as ready for review March 18, 2024 16:29
@FriederikeHanssen
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This PR scares me :D What are the output files now called?

maxulysse
maxulysse approved these changes Mar 18, 2024
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<3

@FriederikeHanssen
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Before merging, can you test on the full size test? I am worried that the output name changing of the bed file could have effects we don't see on a smaller dataset. in the earlier days of sarek 3, we had issues in that direction

@asp8200
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asp8200 commented Mar 18, 2024

This PR scares me :D What are the output files now called?

I don't think the bed-file is or were published, but the output-file in the work-folder is called genome.fasta.bed. This is the .command.sh in the case of the simple test-profile with no supplied interval/bed :

awk \
    -v FS='     ' -v OFS='      ' '{ print $1, "0", $2 }' \
     \
    genome.fasta.fai \
    > genome.fasta.bed

The following is the .command.sh in the case of the simple test-profile with no supplied interval/bed - executed from the dev-branch:

awk -v FS='     ' -v OFS='      ' '{ print $1, "0", $2 }' genome.fasta.fai > genome.fasta.bed

@FriederikeHanssen
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no they are not published but they are used further in the pipeline.

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asp8200 commented Mar 18, 2024 •
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Before merging, can you test on the full size test? I am worried that the output name changing of the bed file could have effects we don't see on a smaller dataset. in the earlier days of sarek 3, we had issues in that direction

Sure I can run the full-test. Better safe than sorry. Anything, in particular, I should pay attention to in my run of the full-test or is it fine if it completes without crashing?

EDIT: Shot! I just remembered the full-test is still broken in the dev-branch, and so it will also be broken on my branch :-/ What to do?

@FriederikeHanssen
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I think if it runs through without crashing we are relatively save.

@maxulysse maxulysse mentioned this pull request Apr 3, 2024
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@maxulysse maxulysse merged commit 52b3fff into nf-core:dev Apr 3, 2024
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@asp8200 asp8200 deleted the replace_build_intervals_with_gawk branch June 4, 2024 10:49
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@asp8200 @FriederikeHanssen @maxulysse