nf-core/pneumocat @ 0.0.0-6c4ed3a
Summary
Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
Get started
Add the following snippet to your workflow script to include this module.
include { PNEUMOCAT } from 'nf-core/pneumocat'
License
MIT License
Process
Name
|
PNEUMOCAT |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reads
file
|
Input Illunina paired-end FASTQ files *.{fq.gz,fastq.gz}
|
Output
3 channels
#1
txt
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.txt
file
|
A detailed description of the predicted serotype *.txt
|
#2
xml
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.xml
file
|
The predicted serotype in XML format *.xml
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| pneumocat | PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina) | https://github.com/ukhsa-collaboration/PneumoCaT |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:38:08 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpneumocat/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pneumocat/blobs/sha256:338db9553553946b8d9cd94b99839f0bfec1cdc785337b6f30ce6111b1a5f19e |
| Size | 2.4 KB |
| Checksum | sha256:338db9553553946b8d9cd94b99839f0bfec1cdc785337b6f30ce6111b1a5f19e |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:38:08 (UTC) | 3 | 2.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:27:17 (UTC) | 3 | 2.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:27:59 (UTC) | 3 | 2.4 KB |