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PROFILES: test -> test_cache + restore test #1026

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Merged
drpatelh merged 5 commits into from
May 25, 2023
Merged

PROFILES: test -> test_cache + restore test #1026

drpatelh merged 5 commits into from
May 25, 2023

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@maxulysse
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@maxulysse maxulysse commented May 15, 2023

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/rnaseq 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 May 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cfe179a

+| ✅ 150 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-23 11:39:02

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maxulysse commented May 15, 2023

Logic behind this PR is to keep profile test as a works everywhere/resolve everywhere profile.
The underlying logic with params.test_data_base, makes it complicated to resolve config properly and can hide params.
I'd then recommend to have 2 profiles (which would actually be the same once all params and path are resolved), but one that can work as is, without any resolving issues (historical test profile), and the other from which we can change provenance of files (test_cache profile).

drpatelh
drpatelh reviewed May 15, 2023
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drpatelh
drpatelh reviewed May 23, 2023
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@maxulysse @drpatelh
Update conf/test.config
cfe179a 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
drpatelh
drpatelh approved these changes May 25, 2023
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Thanks @maxulysse ! I'll make the remaining changes in a follow up PR.

conf/test_cache.config
@@ -0,0 +1,50 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
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@drpatelh drpatelh May 23, 2023

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Suggested change
Nextflow config file for running minimal tests
Nextflow config file for running minimal tests using cached / offline test data

@drpatelh drpatelh merged commit 9472aaa into nf-core:dev May 25, 2023
@maxulysse maxulysse deleted the profile_test_data_base branch May 25, 2023 12:16
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