specify the relative abundance of each known haplotype
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
variants{:bash}
:file
File containing identified variants in a gff-like format
*.variants.tsv
depths{:bash}
File containing depth of the variants
*.depth.tsv
barcodes{:bash}
File containing lineage defining barcodes
*barcodes.csv
lineages_meta{:bash}
Optional file containing lineage metadata that correspond to barcodes
*lineages.json
lineages_topology{:bash}
Optional file containing lineage topology information that correspond to barcodes
*lineages.yml
demix{:bash}
*.tsv{:bash}
a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation
*.demix.tsv
versions_freyja{:bash}
${task.process}{:bash}
:string
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.
