nf-core/freyja/boot @ 0.0.0-0c7146d
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
Name
|
FREYJA_BOOT |
|---|
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
|
|---|
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
|
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
|
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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:40:09 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ffreyja%2Fboot/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/freyja/boot/blobs/sha256:07b16dccf82ffb96785b0171bf1f937b53d16ed95b01727821f673cc22850231 |
| Size | 3.1 KB |
| Checksum | sha256:07b16dccf82ffb96785b0171bf1f937b53d16ed95b01727821f673cc22850231 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:40:09 (UTC) | 1 | 3.1 KB | - |