Updating an existing case using the command line interface

A case in the scout db can be updated after loading. Best practica involves making a new scout load config, and proceeding to upload with scout load case -u my_new_config.yaml, but occasionally a specific attribute can be altered instead with the scout update case command.

``` Usage: scout update case [OPTIONS] [CASE_ID]

Update a case in the database

Options: -n, --case-name TEXT Search case by display name (institute ID should also be provided) -i, --institute TEXT Case institute ID (case display name should also be provided) -c, --collaborator TEXT Add a collaborator to the case --fraser TEXT Path to clinical WTS OMICS outlier FRASER TSV file to be added - NB variants are NOT loaded --outrider TEXT Path to clinical WTS OMICS outlier OUTRIDER TSV file to be added - NB variants are NOT loaded --rna-genome-build [37|38] RNA human genome build - should match RNA alignment files and IGV tracks --vcf PATH Path to clinical VCF file to be added - NB variants are NOT loaded --vcf-sv PATH path to clinical SV VCF file to be added --vcf-str PATH Path to clinical STR VCF file to be added - NB variants are NOT loaded --vcf-cancer PATH Path to clinical cancer VCF file to be added - NB variants are NOT loaded --vcf-cancer-sv PATH Path to clinical cancer structural VCF file to be added - NB variants are NOT loaded --vcf-research PATH Path to research VCF file to be added - NB variants are NOT loaded --vcf-sv-research PATH Path to research VCF with SV variants to be added --vcf-cancer-research PATH Path to research VCF with cancer variants to be added - NB variants are NOT loaded --vcf-cancer-sv-research PATH Path to research VCF with cancer structural variants to be added - NB variants are NOT loaded --vcf-mei PATH Path to clinical mei variants to be added - NB variants are NOT loaded --vcf-mei-research PATH Path to research mei variants to be added - NB variants are NOT loaded --reupload-sv Remove all SVs and re upload from existing files --rankscore-treshold TEXT Set a new rank score treshold if desired --sv-rankmodel-version TEXT Update the SV rank model version --help Show this message and exit. ```