Midnight update - 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

9 stars 6 forks source link

Midnight update #21

Closed JD2112 closed 2 years ago

JD2112 commented 2 years ago

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

WHAT

change nanopore default analysis with 'midnight' protocol
pangolin updated to latest version (v3.1.11)

WHY

'midnight' requires different primer-schema than 'artic'
needs update for pangolin

HOW

nanopore.config file changes for min_length and max_length of midnight primers
environment file updated for illumina and singularity file updated to run pangolin in nanopore analysis
New singularity containers built for both illumina and nanopore.
README updated; ConnerLab-instructions moved to other markdown file and 'HOW TO USE PIPELINE' wiki page created.
workflow images add to the directory.