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Fixed current Zenodo URL of Kmerfinderdb #157

Merged
merged 2 commits into from
Aug 30, 2024
Merged

Fixed current Zenodo URL of Kmerfinderdb #157

merged 2 commits into from
Aug 30, 2024

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Daniel-VM
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@Daniel-VM Daniel-VM commented Aug 29, 2024 •
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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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/bacass 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).

PR description

This PR attemps to fix corrupted Zenodo Link of Kmerfinder database (fixed version here: https://zenodo.org/records/13447056).

Command to test it

nextflow run main.nf \          
    -profile docker,test \
    --outdir ./results \
    --assembler 'unicycler' \
    --assembly_type 'short' \
    --skip_kmerfinder false \
    --kmerfinderdb 'https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz' \
    --ncbi_assembly_metadata 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt' \
    --skip_annotation -resume

Related #155

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github-actions bot commented Aug 29, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 82adb62

+| ✅ 198 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-29 08:22:27

@Daniel-VM Daniel-VM marked this pull request as ready for review August 29, 2024 09:11
@Daniel-VM Daniel-VM merged commit 5f64486 into nf-core:dev Aug 30, 2024
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@Daniel-VM
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Thanks @jfy133 🙌🏾

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@jfy133 jfy133 jfy133 approved these changes

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@Daniel-VM @jfy133