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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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fix: update to artic 1.2.2 #118

Open thomasbtf opened 2 years ago

thomasbtf commented 2 years ago

The version muscle used in artic was set to >=3.8. As muscle published version 5.1, the newer version is now used. However, the 5.1 version has a different clit which breaks artic and thus ncov2019-artic-nf:

Running: muscle -in some.muscle.in.fasta -out some.muscle.out.fasta

Invalid command line
Unknown option in

This PR updates the artic version, which includes a bug fix for the problem described above.

See https://github.com/artic-network/fieldbioinformatics/issues/105 for more information.