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Deactivate CONCOCT to make reasonable AWS full test run time#441

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jfy133 merged 2 commits intodevfrom
deactivate-full-test-concoct
May 11, 2023
Merged

Deactivate CONCOCT to make reasonable AWS full test run time#441
jfy133 merged 2 commits intodevfrom
deactivate-full-test-concoct

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@jfy133 jfy133 commented May 11, 2023 •
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As the easiest and more value-for-money solution

Closes #403

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).

@jfy133 jfy133 linked an issue May 11, 2023 that may be closed by this pull request
Deactivate CONCOCT binning from full tests #403
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github-actions Bot commented May 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2c7f437

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • 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 2.8
  • Run at 2023-05-11 07:37:29

jfy133
jfy133 commented May 11, 2023
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Comment thread CHANGELOG.md Outdated

- [#428](https://github.com/nf-core/mag/pull/428) - Update to nf-core 2.8 `TEMPLATE` (by @jfy133)
- [#429](https://github.com/nf-core/mag/pull/429) - Replaced hardcoded CheckM database auto-download URL to a parameter (reported by @erikrikarddaniel, fix by @jfy133)
- [#440](https://github.com/nf-core/mag/pull/429) - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
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Suggested change
- [#440](https://github.com/nf-core/mag/pull/429) - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
- [#441](https://github.com/nf-core/mag/pull/441) - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).

Comment thread CHANGELOG.md Outdated
@jfy133 jfy133 mentioned this pull request May 11, 2023
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erikrikarddaniel
erikrikarddaniel approved these changes May 11, 2023
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👍

@jfy133 jfy133 merged commit d10eab0 into dev May 11, 2023
@jfy133 jfy133 deleted the deactivate-full-test-concoct branch May 11, 2023 10:05
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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

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Deactivate CONCOCT binning from full tests

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