nf-core/cafe @ 0.0.0-0c7146d
Summary
Analysis of gene family evolution
Get started
Add the following snippet to your workflow script to include this module.
include { CAFE } from 'nf-core/cafe'
License
MIT License
Process
Name
|
CAFE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
infile
file
|
Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder) *.{txt,tsv,tab}
|
tree
file
|
Newick formatted tree *.{txt}
|
|---|
Output
6 channels
#1
cafe
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
${prefix}
directory
|
A folder with all the cafe output |
#2
cafe_report
$prefix/*_report.cafe
file
|
File containing the final report from cafe *_report.cafe
|
|---|
#3
cafe_results
$prefix/*results.txt
file
|
File containing the main result files from cafe *results.txt
|
|---|
#4
versions_cafe
tuple
${task.process}
string
|
The name of the process |
|---|---|
cafe
string
|
The name of the tool |
echo 5.1.0
eval
|
The expression to obtain the version of the tool |
#5
cafe_base_count
$prefix/*_count.tab
file
|
File containing counts of genes per orthogroup *_count.tab
|
|---|
#6
cafe_significant_trees
$prefix/*.tre
file
|
File containing significant trees (newick format) *.tre
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| cafe | Computational Analysis of gene Family Evolution (CAFE) | https://github.com/hahnlab/CAFE5 |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:29:06 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcafe/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cafe/blobs/sha256:f66f30b119b30ee4d2a3d286372d87b5705736ee6e0be0d91ffacf17810ce4e1 |
| Size | 3.1 KB |
| Checksum | sha256:f66f30b119b30ee4d2a3d286372d87b5705736ee6e0be0d91ffacf17810ce4e1 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:29:06 (UTC) | 1 | 3.1 KB | - |