call variant and sequencing depth information of the variant
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
bam{:bash}
:file
Sorted BAM file
*.bam
fasta{:bash}
The reference sequence used for mapping and generating the BAM file
*.fa
variants{:bash}
*.variants.tsv{:bash}
File containing identified variants in a gff-like format
*.variants.tsv
*.depth.tsv{:bash}
File containing depth of the variants
*.depth.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.
