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 (value (int))

Number of bootstrap repeats to perform

val_db_name (value (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
included modules and subworkflows
freyja/variants freyja/demix freyja/update freyja/boot
maintainer
Github user Joon-Klaps
get in touch
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