Description

Pacbio ccs - Generate Higly Accurate Single-Molecule Consensus Reads

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information id: id of the split file

bam:file

Raw subreads bam

*.subreads.bam

pbi:file

Pacbio BAM Index

*.pbi

chunk_num:integer

BAM part to process

chunk_on:integer

Total number of bam parts to process

Output

name:type
description
pattern

bam

meta:map

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

]

*.chunk*.bam:file

CCS sequences in bam format

*.bam

pbi

meta:map

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

]

*.chunk*.bam.pbi:file

PacBio Index of CCS sequences

*.pbi

report_txt

meta:map

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

]

*.report.txt" :file

Summary of CCS in txt format

.txt

report_json

meta:map

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

]

*.report.json" :file

Summary of CCS in txt json

.json

metrics

meta:map

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

]

*.metrics.json.gz:file

Metrics about zmws

*.json.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

pbccs
BSD-3-Clause-Clear

pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)