Description

Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)

Input

name:type
description
pattern

ch_bam :file

Structure: [ val(meta), path(bam) ]
Groovy Map containing sample information e.g. [ id:‘test’, single_end

] and sorted BAM file

ch_fasta :file

Structure: [ val(meta), path(fasta) ]
Groovy Map containing sample information e.g. [ id:‘test’, single_end

] and the fasta reference used for the sorted BAM file

val_repeats :integer

Number of bootstrap repeats to perform

val_db_name :string

Name of the dir where UShER’s files will be stored

ch_barcodes :file

Structure: path(barcodes)
File containing lineage defining barcodes

ch_lineages_meta :file

Structure: path(lineages_meta)
File containing lineage metadata that correspond to barcodes

Output

name:type
description
pattern

meta :map

Groovy Map containing sample information
e.g. [ id:‘test’ ]

variants :file

Structure: [ val(meta), path(variants) ]
File containing identified variants in a gff-like format

depths :file

Structure: [ val(meta), path(variants) ]
File containing depth of the variants

demix :file

Structure: [ val(meta), path(demix) ]
a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation

lineages :file

Structure: [ val(meta), path(lineages) ]
a csv file that includes the lineages present and their corresponding abundances

summarized :file

Structure: [ val(meta), path(lineages) ]
a csv file that includes the lineages present but summarized by constellation and their corresponding abundances

barcodes :file

path(barcodes) a csv file that includes the lineages present but summarized by constellation and their corresponding abundances

lineages_meta :file

path(lineages_meta) a csv file that includes the lineages present but summarized by constellation and their corresponding abundances

versions :file

File containing software versions

versions.yml