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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Have the possibility to add a reference sequence as root for nextclade #69

Open pbiology opened 1 year ago

pbiology commented 1 year ago

What needs to be done: Next clade accepts a fasta file as root sequence for the nextclade typing. As is, gms-artic is using the default settings (I think). It would be nice if the user could specify a sequence (or strain name) and the ref sequence and reference tree was set to this. Without any inputs it should do as it does now to not break anything for other users.

Nextclade input documentation here: https://docs.nextstrain.org/projects/nextclade/en/stable/user/input-files.html#reference-root-sequence

Suggestions on how to get it done:

What are the arguments for getting it done: The user then has more flexibility as to what sequence to root with

Task is considered finished when: ref-sequence and ref-tree is set from command line

pbiology commented 1 year ago

Is this perhaps already possible just as nextflow arguments? @JD2112 and @sofstam?