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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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Jd2112 nextclade #15

Closed JD2112 closed 3 years ago

JD2112 commented 3 years ago

What

I've added the support for Nextclade to identify differences between the input sequences and reference sequences used by Nextstrain as well as reports potential sequence quality issues in the input sequence. It also describes the clades which are defined by specific signature mutations as defined by Nextstrain.

Why

This will give the information if the clades are groups of related sequences that share a common ancestor and uses the phylogenetic context to assign clades.

How

I've added the NextcladeJS to the conda dependency in the environment.yml files for both Illumina and Nanopore workflows. process nextclade is added to the /modules/typing.nf and also the process included in the workflows/illuminaNcov.nf and workflows/articNcovNanopore.nf.

Testing

I've tested the process nextclade with a full run of the pipeline in the local machine as well as NGP server for both Illumina and Nanopore test data and both are working fine. @sylvinite

sofstam commented 2 years ago

@sylvinite @JD2112 Is there a reason that nextclade_js (https://anaconda.org/bioconda/nextclade_js) was used instead of nextclade (https://anaconda.org/bioconda/nextclade)? Or am I missing something here?