modules/star_starsolo

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

aligncountgenomereference

https://github.com/nf-core/modules/[...]/modules/nf-core/star/starsolo

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.

`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

`meta2`
`:map`

Groovy Map containing the STAR index information.

`index`
`:directory`

STAR genome index

star

Output

name:type

description

pattern

`counts`

`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

`log_final`

`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

`log_out`

`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

`log_progress`

`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

`summary`

`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

`versions`

`versions.yml`
`: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

modules/star_starsolo

Description

Input

`meta`
`:map`

`solotype`
`:string`

`reads`
`:file`

`opt_whitelist`
`:file`

`meta2`
`:map`

`index`
`:directory`

Output

`counts`

`meta`
`:map`

`*.Solo.out`
`:file`

`log_final`

`meta`
`:map`

`*Log.final.out`
`:file`

`log_out`

`meta`
`:map`

`*Log.out`
`:file`

`log_progress`

`meta`
`:map`

`*Log.progress.out`
`:file`

`summary`

`meta`
`:map`

`*/Gene/Summary.csv`
`:file`

`versions`

`versions.yml`
`:file`

Tools

starsolo
MIT

maintainers

get in touch

modules/star_starsolo

Description

Input

meta:map

solotype:string

reads:file

opt_whitelist:file

meta2:map

index:directory

Output

counts

meta:map

*.Solo.out:file

log_final

meta:map

*Log.final.out:file

log_out

meta:map

*Log.out:file

log_progress

meta:map

*Log.progress.out:file

summary

meta:map

*/Gene/Summary.csv:file

versions

versions.yml:file

Tools

starsolo MIT

maintainers

get in touch

`meta`
`:map`

`solotype`
`:string`

`reads`
`:file`

`opt_whitelist`
`:file`

`meta2`
`:map`

`index`
`:directory`

`counts`

`meta`
`:map`

`*.Solo.out`
`:file`

`log_final`

`meta`
`:map`

`*Log.final.out`
`:file`

`log_out`

`meta`
`:map`

`*Log.out`
`:file`

`log_progress`

`meta`
`:map`

`*Log.progress.out`
`:file`

`summary`

`meta`
`:map`

`*/Gene/Summary.csv`
`:file`

`versions`

`versions.yml`
`:file`

starsolo
MIT