v2.0-separated containers and new features

Pangolin container separated and new features for Illumina and Nanopore analysis

1. Docker container separated for Pangolin typing

• Illumina container: gms-artic-illumina
• Nanopore container: gms-artic-nanopore
• Pangolin container: gms-artic-pangolin
• pycoQC container : pycoqc

2. Added separate package version files for each workflow versions: for Illumina and Nanopore
3. pangoversion: for pangolin typing
4. Illumina analysis additional features
   • flagstat
   • depth
   • VEP annotation
5. Illumina results works for sc2reporter visualization
6. Nanopore analysis additional features (artic & medaka)

• fastqc
• multiqc
• pycoQC (only for artic)

QC and deployment

Minor updates

• Pangolin v4 support
• Updated Picard arguments
• FastQC commands can be added from config
• Added version of pangolin to build_dockerfile

Bug fixes

• Fixed build_dockerfile
• Fixed R issue
• Fixed mamba issue

Primer-scheme updated

1. Primer scheme updated for Nanopore run. Current repo will download the primer sets from gms-repo.
2. --scheme is required to run the Nanopore analysis
3. Illumina run set as before.
4. containers will be updated every 2 weeks
5. Nextclade version updated.

Software versions

• Added software versions output file

GHaction setup

1. Latest updates for Pangolin version each day with GH action
2. genomicmedicinesweden DockerHub integration
3. Build docker containers with latest version
4. Nanopore Medaka workflow running with container and pangolin version

nanopore update with midnight protocol

1. midnight protocol set as the default nanopore analysis
2. pangolinTyping updated to latest release