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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
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update of env.yml for medaka v1.0.3 and dependencies #55

Closed sagrudd closed 4 years ago

sagrudd commented 4 years ago

Hi Will and Nick - update of MinKNOW and the underlying guppy version brings new error models - now would be a good time to update the included version of Medaka. Medaka now requires HTSLIB 1.10 - I have therefore amended the versions of samtools, bcftools and pysam (and included an explicit version of htslib). I have tested on a couple of systems - thanks for the consideration

nickloman commented 4 years ago

Thanks @sagrudd @will-rowe Can you review?

will-rowe commented 4 years ago

Just to give an update to @sagrudd

Environment change looks good and doesn't impact the Nanopore workflow. The issue is that the new medaka version is giving us a new variant being reported (11074 . CT C) in some of the test data, and we're also seeing altered consensus sequences. This is causing the tests to fail, which might not be a problem but we want to work out why this change has occurred before updating the software versions.

Will keep you posted.

will-rowe commented 4 years ago

We need to tweak the medaka commands to get this update to work - will file a PR and then check back here

will-rowe commented 4 years ago

Looks good - thanks @sagrudd!