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Pacbio fastq #106

Merged
merged 4 commits into from
Aug 15, 2024
Merged

Pacbio fastq #106

merged 4 commits into from
Aug 15, 2024

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tkchafin
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Addresses #101

  • Adds fastq (fq.gz or fastq.gz) as input options for PacBio
  • Converted one of the test profile pacbio files to fastq for testing
  • simplified filter_pacbio.nf a bit using multiMap
  • Note this version still uses blastn for filtering

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
  • 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).

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@BethYates BethYates left a comment

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Looks great - thanks!

@tkchafin tkchafin merged commit 02660d4 into sanger-tol:dev Aug 15, 2024
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@tkchafin tkchafin deleted the pacbio_fastq branch August 15, 2024 08:28
@tkchafin tkchafin mentioned this pull request Aug 20, 2024
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2 participants