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sanjaynagi / AmpSeeker

A state-of-the-art snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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Implement snpeff annotation, snp-df nb and process nbs #82

Closed sanjaynagi closed 11 months ago

sanjaynagi commented 11 months ago

This PR will resolve #80 #81 and #71.

  1. We introduce Snpeff for variant annotation. db is specified in the config.
  2. We implement a notebook, snp-dataframe, which converts vcf to dataframe and .xlsx
  3. We add a notebook, process-notebooks, which adds a cell tag to each nb, so that papermills injected parameters do not show up in the results-book.

@ChabbyTMD Please take a look when you can. I've also made some changes over the last day or two, adding whole amplicon variant calling #78 and a welcome message when starting the workflow #76 .