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Fix --skip_busco#256

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d4straub merged 9 commits intonf-core:devfrom
d4straub:fix-skip_busco
Nov 23, 2021
Merged

Fix --skip_busco#256
d4straub merged 9 commits intonf-core:devfrom
d4straub:fix-skip_busco

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@d4straub d4straub commented Nov 22, 2021 •
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Closes #232
Currently the gtdb database "https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz" is not accessible, the mirror "https://data.ace.uq.edu.au/public/gtdb/data/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz" works however.
I changed the default from data.gtdb.ecogenomic.org to data.ace.uq.edu.au now.

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).
  • 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 Nov 22, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b45414b

+| ✅ 136 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-23 09:31:27

ggabernet
ggabernet approved these changes Nov 23, 2021
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Looks good to me

Comment thread lib/WorkflowMag.groovy Outdated
@d4straub @ggabernet
Update lib/WorkflowMag.groovy
b45414b 
Co-authored-by: Gisela Gabernet <[email protected]>
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d4straub commented Nov 23, 2021

Thanks!

@d4straub d4straub merged commit 2caec7c into nf-core:dev Nov 23, 2021
@d4straub d4straub deleted the fix-skip_busco branch November 23, 2021 10:16
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