Description

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

Input

Name (Type)
Description
Pattern

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.

meta2 (map)

Groovy Map containing the STAR index information.

index (directory)

STAR genome index

star

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

Output

Name (Type)
Description
Pattern

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 (file)

STAR final log file

*Log.final.out

log_out (file)

STAR lot out file

*Log.out

log_progress (file)

STAR log progress file

*Log.progress.out

summary (file)

STARSolo metrics summary CSV file.

*/Gene/Summary.csv

versions (file)

File containing software versions

versions.yml
authors
Github user kevinmenden Github user ggabernet Github user grst Github user fmalmeida Github user rhreynolds Github user apeltzer Github user vivian-chen16 Github user maxulysse Github user joaodemeirelles
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

starsolo
MIT

Mapping, demultiplexing and quantification for single cell RNA-seq.

github.com/alexdobin/STAR github.com/alexdobin/STAR/blob/master/docs/STARsolo.md 10.1101/2021.05.05.442755