nf-core/freyja/variants @ 0.0.0-0c7146d
Summary
call variant and sequencing depth information of the variant
Get started
Add the following snippet to your workflow script to include this module.
include { FREYJA_VARIANTS } from 'nf-core/freyja/variants'
License
MIT License
Process
Name
|
FREYJA_VARIANTS |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
bam
file
|
Sorted BAM file *.bam
|
fasta
file
|
The reference sequence used for mapping and generating the BAM file *.fa
|
|---|
Output
2 channels
#1
variants
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.variants.tsv
file
|
File containing identified variants in a gff-like format *.variants.tsv
|
*.depth.tsv
file
|
File containing depth of the variants *.depth.tsv
|
#2
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 18:40:14 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ffreyja%2Fvariants/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/freyja/variants/blobs/sha256:09a4c341e041db6bd1ecee18540bcd1ef88c566fa12f94704a836406ff236a6e |
| Size | 2.4 KB |
| Checksum | sha256:09a4c341e041db6bd1ecee18540bcd1ef88c566fa12f94704a836406ff236a6e |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:40:14 (UTC) | 1 | 2.4 KB | - |