nf-core/biomformat/convert @ 0.0.0-0c7146d
Summary
Convert biom table to different format. Conversion between text tab-delimited, BIOM-v1 (JSON), and BIOM-v2 (HDF5) formats are supported
Get started
Add the following snippet to your workflow script to include this module.
include { BIOMFORMAT_CONVERT } from 'nf-core/biomformat/convert'
License
MIT License
Process
Name
|
BIOMFORMAT_CONVERT |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
biom
file
|
Biom formatted feature table file *.{biom,txt,tsv}
|
Output
3 channels
#1
txt
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.txt
file
|
Converted txt file *.txt
|
#2
biom
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.biom
file
|
Converted biom file *.biom
|
#3
versions_biomformat
tuple
${task.process}
string
|
The name of the process |
|---|---|
biom-format
string
|
The name of the tool |
biom --version | sed 's/biom, version //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| biomformat | Biological Observation Matrix (BIOM) format. This package includes basic tools for converting, summarizing, and adding metadata to biom-format files. | http://biom-format.org/index.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:27:00 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbiomformat%2Fconvert/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/biomformat/convert/blobs/sha256:c78e41ef600c658441ff99bb77802441e99c30905f00893c52d140ab379fa2ea |
| Size | 3.1 KB |
| Checksum | sha256:c78e41ef600c658441ff99bb77802441e99c30905f00893c52d140ab379fa2ea |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:27:00 (UTC) | 1 | 3.1 KB | - |