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Use edlib global alignment to generate SNP report #39

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@nhhaidee nhhaidee commented Aug 11, 2023

Changes

  • edlib global alignment of consensus sequence against user sequences instead of blastn local alignment
  • snp report includes mismatches, indels, edit distance information obtained from Global Alignment
  • Output details of alignment for each segment including nice alignment path, Multi QC report

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 - ensure that you've added the version info to a versions.yml and added it to the ch_versions channel in the workflow you added the tool to.
    • 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 CFIA-NCFAD/nf-test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test_{illumina,nanopore},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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