Description

Extract UMI and cell barcodes

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

bam:file

BAM file, one full-length CCS file generated by lima

*.5p--3p.bam

design:string

Barcoding design. Specifies which bases to use as cell/molecular barcodes.

^(?:\d{1,2}[UBGX]-)+T$|^(?:\d{1,2}[UBGX]-)+T(?:-\d{1,2}[UBGX])+$|^T(?:-\d{1,2}[UBGX])+$

Output

name:type
description
pattern

bam

meta:map

Groovy Map containing sample information e.g. [ id:'sample1']

*.flt.bam:file

BAM file with full-length tagged reads

*.flt.bam

pbi

meta:map

Groovy Map containing sample information e.g. [ id:'sample1']

*.flt.bam.pbi:file

Pacbio index file of full-length tagged reads

*.flt.bam.pbi

versions

versions.yml:file

File containing software versions

versions.yml