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niemasd / ViReflow

An elastically-scaling automated AWS pipeline for viral consensus sequence generation
GNU General Public License v3.0
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Add pTrimmer #5

Closed niemasd closed 3 years ago

niemasd commented 3 years ago

pTrimmer GitHub repo:

https://github.com/DMU-lilab/pTrimmer

I've already created a Docker image (niemasd/ptrimmer):

https://hub.docker.com/r/niemasd/ptrimmer

However, pTrimmer doesn't use a standard BED or FASTA, but rather, it uses their own proprietary TXT format to represent primer sequences:

https://github.com/DMU-lilab/pTrimmer#input

I don't feel like figuring out how to convert from BED + reference genome sequence to this format (yet), but I should in the future

niemasd commented 3 years ago

Created a GitHub Issue on the pTrimmer repo to see if there's a known simple way to do this:

https://github.com/DMU-lilab/pTrimmer/issues/15

niemasd commented 3 years ago

Added in ViReflow v1.0.7

https://github.com/niemasd/ViReflow/commit/fa32796af312f312d7f65c70cf339b16b48c2dbc