Description

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

Input

name:type
description
pattern

meta{:bash}

: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{:bash}

: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{:bash}

:file

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

opt_whitelist{:bash}

:file

Optional whitelist file

meta2{:bash}

:map

Groovy Map containing the STAR index information.

index{:bash}

:directory

STAR genome index

star

Output

name:type
description
pattern

counts{:bash}

meta{:bash}

: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{:bash}

:file

STARSolo counts matrix

*.Solo.out

log_final{:bash}

meta{:bash}

: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{:bash}

:file

STAR final log file

*Log.final.out

log_out{:bash}

meta{:bash}

: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{:bash}

:file

STAR lot out file

*Log.out

log_progress{:bash}

meta{:bash}

: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{:bash}

:file

STAR log progress file

*Log.progress.out

summary{:bash}

meta{:bash}

: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{:bash}

:file

STARSolo metrics summary CSV file.

*/Gene/Summary.csv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainers
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
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