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fix intervals checks #650

Merged
merged 4 commits into from
Jul 18, 2022
Merged

fix intervals checks #650

merged 4 commits into from
Jul 18, 2022

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maxulysse
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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).

@maxulysse
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Got a warning about intervals while running --step annotate

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github-actions bot commented Jul 18, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6f481bb

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • 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: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-18 07:21:06

FriederikeHanssen
FriederikeHanssen reviewed Jul 18, 2022
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conf/test.config
@@ -54,6 +54,7 @@ profiles {
params.step = 'annotate'
}
no_intervals {
params.intervals = null
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do we need to add the same to the nextflow config/ some logic for params.no_intervals?

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I'm assuming that people specifying --no_intervals mostly do that with a custom genome, and don't provide --intervals then.
Worst case for people using --no_intervals and iGenomes for genomes where we do provide intervals, we have just this warning.

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ok

asp8200
asp8200 approved these changes Jul 18, 2022
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Looks fine to me.

@FriederikeHanssen FriederikeHanssen merged commit c43ef33 into nf-core:dev Jul 18, 2022
@maxulysse maxulysse deleted the dev_intervals_checks branch July 18, 2022 08:34
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@asp8200 asp8200 asp8200 approved these changes

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@maxulysse @FriederikeHanssen @asp8200