downloads new versions of the curated SARS-CoV-2 lineage file and barcodes
db_name{:bash}
:string
The name of the database directory
barcodes{:bash}
${db_name}/*barcodes.*{:bash}
:file
File containing lineage defining barcodes
*barcodes.csv
lineages_topology{:bash}
${db_name}/*lineages.yml{:bash}
File containing lineage topology information that correspond to barcodes
*lineages.yml
lineages_meta{:bash}
${db_name}/*curated_lineages.json{:bash}
File containing lineage metadata that correspond to barcodes
*curated_lineages.json
config{:bash}
${db_name}/*pathogen_config.yml{:bash}
File containing pathogen configuration information for Freyja
*pathogen_config.yml
versions_freyja{:bash}
${task.process}{:bash}
The name of the process
freyja{:bash}
The name of the tool
freyja --version | sed 's/.* //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
