nf-core/biomformat/convert @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:06:11 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbiomformat%2Fconvert/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/biomformat/convert/blobs/sha256:a0968b2f2c11e3aa577a23446bbc7c953186dd5b7601fa0c6ee16dd12afd18a1 |
| Size | 3.1 KB |
| Checksum | sha256:a0968b2f2c11e3aa577a23446bbc7c953186dd5b7601fa0c6ee16dd12afd18a1 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:06:11 (UTC) | 4 | 3.1 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:04:13 (UTC) | 3 | 3.1 KB | |
| 0.0.0-7f68141 | 16 Apr 2026 15:00:11 (UTC) | 4 | 3.1 KB | |
| 0.0.0-02a6b4c | 13 Apr 2026 15:00:10 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:47:45 (UTC) | 3 | 3.1 KB |