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)

bamvariantscram

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_variant_demix_boot_freyja

Description

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

Input

name

description

pattern

`ch_bam`

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

`ch_fasta`

Structure: [ val(meta), path(fasta) ]
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ] and the fasta reference used for the sorted BAM file

`val_repeats`

Number of bootstrap repeats to perform

`val_db_name`

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

`ch_barcodes`

Structure: path(barcodes)
File containing lineage defining barcodes

`ch_lineages_meta`

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

Output

name

description

pattern

`meta`

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

`variants`

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

`depths`

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

`demix`

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

`lineages`

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

`summarized`

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

`barcodes`

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

`lineages_meta`

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

`versions`

File containing software versions

versions.yml