Specify pangolin version via variable at docker build - 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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Specify pangolin version via variable at docker build #60

Closed dodslaser closed 1 year ago

dodslaser commented 2 years ago

The pangolin container is hardcoded to download v3.1.14. This leads to different pangolin versions being reported in the pipeline output (since the nanopore container has the latest version). The pangolin containers on DockerHub tagged with the later pangolin versions (eg. p-4.1.1) currently contain v3.1.14.

The purpose of the code changes are as follows:

Ensures the latest pangolin version is downloaded at docker build of the pangolin container
Ensures that the pangolin version is consistent throughout the pipeline and in the container tag
Minor tweaks to ensure the automatic builds are compatible with pangolin v4.x.x

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

sofstam commented 1 year ago

I close this PR. It has been merged https://github.com/genomic-medicine-sweden/gms-artic/pull/61