nf-core/kallistobustools/count @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:50:47 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fkallistobustools%2Fcount/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/kallistobustools/count/blobs/sha256:acd189d9260e31e9153e67ecb69aa0cf26bec9f5e16a7d275c94d0c4261517e0 |
| Size | 3.9 KB |
| Checksum | sha256:acd189d9260e31e9153e67ecb69aa0cf26bec9f5e16a7d275c94d0c4261517e0 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:50:47 (UTC) | 1 | 3.9 KB | - |