nf-core/pneumocat @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:04:45 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpneumocat/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pneumocat/blobs/sha256:cc8dd8bc4c288d74cf1e820249e962d43af9e5ceab73a5e8592018abc3d865ec |
| Size | 2.4 KB |
| Checksum | sha256:cc8dd8bc4c288d74cf1e820249e962d43af9e5ceab73a5e8592018abc3d865ec |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:04:45 (UTC) | 1 | 2.4 KB | - |