Join us for our weekly series of short talks: nf-core/bytesize.
Just 15 minutes + questions, we focus on topics about using and developing nf-core
pipelines. These are recorded and made available at https://nf-co.re
, helping to build an archive of training material. Got an idea for a talk? Let us know on the #bytesize
Slack channel!
This week, James Fellows Yates (@jfy133) will tell us all about the nf-core/eager pipeline.
nf-core/eager is one of the largest and/or most complex nf-core pipelines. It is a best practise (meta)genomics primarily aimed at (but not limited to) processing ancient DNA. This talk will:
- Give an overview of the pipeline.
- Discuss the impact of the particularlities of ancient DNA.
- Cover some of the challenges and solutions encountered when writing this pipeline.
Video transcription
Note
The content has been edited to make it reader-friendly
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during seeding. So developing a little tool ecosystem around this that feeds in and out of eager. To cope with the changing standards, I use Twitter, where I use the ‘hive mind’ to assess the general consensus that allows us to improve the various features in the pipeline. I’ve also repeatedly introduced it at workshops; this is very important to capture people from different fields in order to get their feedback on the pipeline.
So to summarise, palaeogenomics is complicated, but it is a fun challenge. Broad documentation helps in interdisciplinary fields. Finally, be active in outreach, not just in support, but to try and sell your pipeline because it keeps your project alive past publication and nf-core/eager will hopefully continue to be used and developed by scientists in the ancient DNA field.