Description

quantifies scRNA-seq data from fastq files using kb-python.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

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 spliced_t2c file

*.{cdna_t2c.txt}

t2c (file)

kb ref’s c2 unspliced_t2c file

*.{introns_t2c.txt}

workflow_mode (string)

String value defining workflow to use, can be one of “standard”, “lamanno”, “nucleus”

{standard,lamanno,nucleus,kite}

technology (string)

String value defining the sequencing technology used.

{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

count (file)

kb count output folder

*.{count}

versions (file)

File containing software versions

versions.yml
included in
scrnaseq
author
Github user flowuenne
get in touch
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Tools

kb
MIT License

kallisto and bustools are wrapped in an easy-to-use program called kb

kallistobus.tools kb-python.readthedocs.io/en/latest/index.html https://github.com/pachterlab/kb_python