Update docker image container and nextflow config - 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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Update docker image container and nextflow config #28

Closed JD2112 closed 2 years ago

JD2112 commented 2 years ago

docker image containers for Illumina (including pangolin), Nanopore and pangolin updated to new Dockerhub genomicmedicinesweden
Nextflow config file default setup changed to docker images from dockerhub genomicmedcinesweden.
Optional singularity containers are still in the code, if needed.
changes are tested on example datasets of both Illumina and nanopore data.

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
[ ] The code has been reviewed by @octocat

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