Nextflow Registry | nf-core/pbccs@0.0.0-6c4ed3a

nf-core/pbccs @ 0.0.0-6c4ed3a

Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads

ccs pacbio isoseq subreads

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @sguizard

Maintainers: @sguizard

Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads

Add the following snippet to your workflow script to include this module.

include { PBCCS } from 'nf-core/pbccs'

MIT License

Process

`Name`	`PBCCS`

Input 3 channels

#1 tuple

`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 6 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`.chunk.bam` file	CCS sequences in bam format `*.bam`

#2 pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`.chunk.bam.pbi` file	PacBio Index of CCS sequences `*.pbi`

#3 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.metrics.json.gz` file	Metrics about zmws `*.json.gz`

#4 versions

`versions.yml` file	File containing software versions `versions.yml`

#5 report_txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.report.txt` file	CCS report in text format `*.report.txt`

#6 report_json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.report.json` file	CCS report in JSON format `*.report.json`

Tool	Description	Homepage
pbccs	pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)	https://github.com/PacificBiosciences/pbbioconda

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:35:16 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpbccs/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pbccs/blobs/sha256:8e7710b58614f68c5ab5fe5328ccff9becf0a7534118783187d10319475b90cf
Size	3.0 KB
Checksum	sha256:8e7710b58614f68c5ab5fe5328ccff9becf0a7534118783187d10319475b90cf
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:35:16 (UTC)	3	3.0 KB
0.0.0-3fc6d40	22 Apr 2026 15:25:21 (UTC)	3	3.0 KB