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sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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Implement GitHub actions CI and add test data #6

Closed sanjaynagi closed 1 year ago

sanjaynagi commented 1 year ago

splitting @ChabbyTMD awesome PR #2 into two - Moving all the CI related comits into this PR instead.

this will close #5.

sanjaynagi commented 1 year ago

This PR adds test data to .test/resources/reads, which is real An. gambiae amplicon data from malariagen.

Currently, it makes the repo quite large in size, so later we may want to remove some samples, or subsample them to reduce file size, and speed of the test workflow.

sanjaynagi commented 1 year ago

BGZIP is not being installed by htslib conda, its not clear atm how to install it, as there is no dedicated conda repo.

it does seem to by on pypi.

sanjaynagi commented 1 year ago

https://github.com/marketplace/actions/pip-installer should be able to use this to install bgzip

sanjaynagi commented 1 year ago

Finally working :')

NB wrappers are a good way to get around dependency conflicts.

sanjaynagi commented 1 year ago

I have now reduced the number of samples to 10 (from 26), in order to reduce overall file size.