nf-core/kallistobustools/count @ 0.0.0-3fc6d40
Summary
quantifies scRNA-seq data from fastq files using kb-python.
Get started
Add the following snippet to your workflow script to include this module.
include { KALLISTOBUSTOOLS_COUNT } from 'nf-core/kallistobustools/count'
License
MIT License
Process
Name
|
KALLISTOBUSTOOLS_COUNT |
|---|
Input
7 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reads
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. |
index
file
|
kb-ref index file (.idx) *.{idx}
|
|---|
t2g
file
|
t2g file from kallisto *t2g.txt
|
|---|
t1c
file
|
kb ref's c1 cdna_t2c file *.{cdna_t2c.txt}
|
|---|
t2c
file
|
kb ref's c2 intron_t2c file *.{intron_t2c.txt}
|
|---|
technology
string
|
String value defining the sequencing technology used. {10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}
|
|---|
workflow_mode
string
|
String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) {standard,lamanno,nac}
|
|---|
Output
3 channels
#1
count
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
*.count
file
|
kb count output folder *.{count}
|
#2
matrix
*.count/*/*.mtx
file
|
file containing the count matrix *.mtx
|
|---|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| kb | kallisto and bustools are wrapped in an easy-to-use program called kb | https://www.kallistobus.tools/ |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:18:41 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fkallistobustools%2Fcount/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/kallistobustools/count/blobs/sha256:190cb6f3689bae76ab90e78da6643a4b6c79d64f16e563189f610d6ba2765ac5 |
| Size | 4.0 KB |
| Checksum | sha256:190cb6f3689bae76ab90e78da6643a4b6c79d64f16e563189f610d6ba2765ac5 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:26:44 (UTC) | 3 | 4.0 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:18:41 (UTC) | 3 | 4.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:12:40 (UTC) | 3 | 3.9 KB |