bam_variant_demix_boot_freyja
Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)
Description
Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)
Input
Structure: [ val(meta), path(bam) ]
Groovy Map containing sample information e.g. [ id:‘test’, single_end
Structure: [ val(meta), path(fasta) ]
Groovy Map containing sample information e.g. [ id:‘test’, single_end
Output
Structure: [ val(meta), path(variants) ]
File containing identified variants in a gff-like format
Structure: [ val(meta), path(demix) ]
a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation
Structure: [ val(meta), path(lineages) ]
a csv file that includes the lineages present and their corresponding abundances
Structure: [ val(meta), path(lineages) ]
a csv file that includes the lineages present but summarized by constellation and their corresponding abundances
path(barcodes) a csv file that includes the lineages present but summarized by constellation and their corresponding abundances
path(lineages_meta) a csv file that includes the lineages present but summarized by constellation and their corresponding abundances