Nextflow Registry | nf-core/star/starsolo@0.0.0-6c4ed3a

nf-core/star/starsolo @ 0.0.0-6c4ed3a

Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information.

align count genome reference

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @kevinmenden @ggabernet @grst @fmalmeida @rhreynolds @apeltzer @vivian-chen16 @maxulysse @joaodemeirelles

Maintainers: @kevinmenden @ggabernet @grst @fmalmeida @rhreynolds @apeltzer @vivian-chen16 @maxulysse @joaodemeirelles

Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information.

Add the following snippet to your workflow script to include this module.

include { STARSOLO } from 'nf-core/star/starsolo'

MIT License

Process

`Name`	`STARSOLO`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information. Here, you should add all the specific barcode/umi information for each sample. e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`
`solotype` string	Type of single-cell library. It can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3, CB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq.
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

`opt_whitelist` file	Optional whitelist file

#3 tuple

`meta2` map	Groovy Map containing the STAR index information.
`index` directory	STAR genome index `star`

Output 6 channels

#1 counts tuple

`meta` map	Groovy Map containing sample information. Here, you should add all the specific barcode/umi information for each sample. e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`
`*.Solo.out` file	STARSolo counts matrix `*.Solo.out`

#2 log_out tuple

`meta` map	Groovy Map containing sample information. Here, you should add all the specific barcode/umi information for each sample. e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`
`*Log.out` file	STAR lot out file `*Log.out`

#3 summary tuple

`meta` map	Groovy Map containing sample information. Here, you should add all the specific barcode/umi information for each sample. e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`
`*/Gene/Summary.csv` file	STARSolo metrics summary CSV file. `*/Gene/Summary.csv`

#4 versions

`versions.yml` file	File containing software versions `versions.yml`

#5 log_final tuple

`meta` map	Groovy Map containing sample information. Here, you should add all the specific barcode/umi information for each sample. e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`
`*Log.final.out` file	STAR final log file `*Log.final.out`

#6 log_progress tuple

`meta` map	Groovy Map containing sample information. Here, you should add all the specific barcode/umi information for each sample. e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]`
`*Log.progress.out` file	STAR log progress file `*Log.progress.out`

Tool	Description	Homepage
starsolo	Mapping, demultiplexing and quantification for single cell RNA-seq.	https://github.com/alexdobin/STAR/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:47:27 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fstar%2Fstarsolo/0.0.0-6c4ed3a/download