Nextflow Registry | nf-core/pbccs@0.0.0-0c7146d

nf-core/pbccs @ 0.0.0-0c7146d

Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads

ccs pacbio isoseq subreads

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:01:34 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpbccs/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pbccs/blobs/sha256:62b5680ef01045c1c7808c0cdfe2a8d41bed0064de783612c377b7b0a924e2b9
Size	3.0 KB
Checksum	sha256:62b5680ef01045c1c7808c0cdfe2a8d41bed0064de783612c377b7b0a924e2b9
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:01:34 (UTC)		1	3.0 KB	-