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nf-core/freyja/boot @ 0.0.0-0c7146d

Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.

variants fasta deconvolution wastewater bootstrapping
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @Joon-Klaps
Maintainers: @Joon-Klaps

Summary

Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth.

Get started

Add the following snippet to your workflow script to include this module.

include { FREYJA_BOOT } from 'nf-core/freyja/boot'

License

MIT License

Process
Name FREYJA_BOOT
Input 5 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
variants file

File containing identified variants in a gff-like format

 *.variants.tsv
depths file

File containing depth of the variants

 *.depth.tsv
repeats integer

Number of bootstrap repeats to perform
barcodes file

File containing lineage defining barcodes

 *barcodes.csv
lineages_meta file

Optional file containing lineage metadata that correspond to barcodes

 *lineages.json
lineages_topology file

Optional file containing lineage topology information that correspond to barcodes

 *lineages.yml
Output 3 channels
#1 lineages tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
*lineages.csv file

a csv file that includes the lineages present and their corresponding abundances

 *lineages.csv
#2 summarized tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
*summarized.csv file

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

 *summarized.csv
#3 versions_freyja tuple
${task.process} string

The name of the process
freyja string

The name of the tool
freyja --version | sed 's/.* //' eval

The expression to obtain the version of the tool
Tool Description Homepage
freyja Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics. https://github.com/andersen-lab/Freyja
Version 0.0.0-0c7146d
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 08 Apr 2026 19:01:47 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Ffreyja%2Fboot/0.0.0-0c7146d/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/freyja/boot/blobs/sha256:ca816120f39684e81767e435ec3ea02b5052366af620073d9004d7a5e1fa072c
Size 3.1 KB
Checksum sha256:ca816120f39684e81767e435ec3ea02b5052366af620073d9004d7a5e1fa072c
Downloads 4
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:17:48 (UTC) 4 3.1 KB
0.0.0-3fc6d40 22 Apr 2026 15:12:31 (UTC) 2 3.1 KB
0.0.0-0c7146d 08 Apr 2026 19:01:47 (UTC)