A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
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.
The version
muscle
used in artic was set to>=3.8
. Asmuscle
published version 5.1, the newer version is now used. However, the 5.1 version has a different clit which breaksartic
and thusncov2019-artic-nf
: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.