Primer scheme - Githubissues

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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Primer scheme #48

Closed JD2112 closed 2 years ago

JD2112 commented 2 years ago

The purpose of the code changes are as follows:

I did a thing

Standard test procedure

[X] The self-test mentioned in the README finished successfully
[X] Produced files contain expected values
[X] The code has been reviewed by @sylvinite

This version is a:

[ ] MAJOR - when you make incompatible API changes
[x] MINOR - when you add functionality in a backwards compatible manner
[ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

sylvinite commented 2 years ago

Looks good. New primer scheme. Renaming to use gms repo. And a minor fix to suggest usage of --scheme option. Rest is just new reference files.

sofstam commented 2 years ago

Before merging, is it ok if we keep the version of nextclade that we are using now, 1.8.1? Or is it a specific reason for updating to 1.10?

JD2112 commented 2 years ago

Before merging, is it ok if we keep the version of nextclade that we are using now, 1.8.1? Or is it a specific reason for updating to 1.10?

There are some bugs fixed with Nextclade v1.10 from the v1.8, so I added this one. https://github.com/nextstrain/nextclade/releases Of course, I can revert to v1.8.

JD2112 commented 2 years ago

@sofstam the GHaction script for nanopore requires --scheme to run the pipeline. Could you please add this to the script?