Mivmir-Scout version upload support/ integration

[torbjorgen]

Description of feature

When adding a scoring config for GENMOD in GICAM scoring context, cg upload scout is gets borked by a too liberal regex in the manifest.yaml file.

        "668": {
            "id": "668",
            "name": "NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE_FOR_GICAM (refinedchamois)",
            "cached": false,
            "process": "NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE_FOR_GICAM",
            "script": "\n    genmod \\\n        score \\\n         \\\n        --family_file refinedchamois.ped \\\n        --score_config rank_model_mivmir_v1.0.ini \\\n        --outfile refinedchamois_score.vcf \\\n        refinedchamois_snv_genmod_models_research_models.vcf\n\n    cat <<-END_VERSIONS > versions.yml\n    \"NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE_FOR_GICAM\":\n        genmod: $(echo $(genmod --version 2>&1) | sed 's/^.*genmod version: //' )\n    END_VERSIONS\n    ",

--score_config rank_model_mivmir_v1.0.ini

cg uploads the GENMOD-GICAM rank config version rather than the GENMOD default version as the GENMOD default version to Scout.

A decision needs to be taken:

• Refactor Raredisease MIVMIR PR to not go with the NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE_FOR_GICAM: syntax or
• Adjust cg scout upload yaml parsing in cg to be less liberal