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Patch 2.3.2#461

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jfy133 merged 6 commits intomasterfrom
patch
Jun 23, 2023
Merged

Patch 2.3.2#461
jfy133 merged 6 commits intomasterfrom
patch

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@jfy133 jfy133 commented Jun 21, 2023

Fixes two things:

  1. AWS megatest paths so the tests will actually run
  2. Apparently I was overzealous with the output renaming in the aDNA workflow, the pyDamage doesn't actually use a prefix even though it was in the modules config, therefore the 'prefix' needs to actually go into the publishDir directive

Again I'll be responsible for upstream pulls (1 is already integrated, 2 in https://github.com/nf-core/mag/actions/runs/5330953133/jobs/9658192844?pr=459)

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/mag 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 Jun 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3499ce0

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.3.2'
  • 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: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-06-22 19:03:02

d4straub
d4straub approved these changes Jun 21, 2023
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Looks good to me.

Comment thread conf/test_full.config
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jfy133 commented Jun 21, 2023

Once we get an ok from @alexhbnr's testd I can attempt the release from my phone 😬

jfy133
jfy133 commented Jun 22, 2023
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Comment thread CHANGELOG.md Outdated
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alexhbnr commented Jun 22, 2023

@jfy133 Seems to work fine!

jfy133
jfy133 commented Jun 22, 2023
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@alexhbnr alexhbnr self-requested a review June 23, 2023 11:36
@jfy133 jfy133 merged commit 66cf53a into master Jun 23, 2023
@jfy133 jfy133 deleted the patch branch June 23, 2023 11:39
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@alexhbnr alexhbnr alexhbnr approved these changes

@d4straub d4straub d4straub approved these changes

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@jfy133 @alexhbnr @d4straub