8000 Replace download_reference.py with NCBI Datasets API implementation (removes `assembly_summary_refseq.txt` dependency) by Daniel-VM · Pull Request #249 · nf-core/bacass · GitHub
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Replace download_reference.py with NCBI Datasets API implementation (removes assembly_summary_refseq.txt dependency) #249

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Replace download_reference.py with NCBI Datasets API implementation (removes assembly_summary_refseq.txt dependency) #249

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…e in kmerfinder

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 pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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

Refactor download_reference.py to remove the ncbi_assembly_metadata parameter dependency and download references directly via the NCBI Datasets API.

Closes #172

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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