Nextflow Registry | nf-core/isoseq/refine@0.0.0-0c7146d

nf-core/isoseq/refine @ 0.0.0-0c7146d

Remove polyA tail and artificial concatemers

isoseq refine ccs pacbio polyA_tail

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @sguizard

Maintainers: @sguizard

Remove polyA tail and artificial concatemers

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

include { ISOSEQ_REFINE } from 'nf-core/isoseq/refine'

MIT License

Process

`Name`	`ISOSEQ_REFINE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test ]
`bam` file	BAM file, cleaned ccs generated by lima `*.bam`

`primers` file	fasta file of primers `*.fasta`

Output 6 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bam` file	Set of complete reads (with polyA tail), where the polyA has been trimmed `*.bam`

#2 pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bam.pbi` file	Pacbio index file from polyA trimmed reads `*.pbi`

#3 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.report.csv` file	Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name) `*.csv`

#4 summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.filter_summary.report.json` file	json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads `*.json`

#5 versions

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

#6 consensusreadset tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.consensusreadset.xml` file	Metadata about read library `*.xml`

Tool	Description	Homepage
isoseq	IsoSeq - Scalable De Novo Isoform Discovery	https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:49:33 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fisoseq%2Frefine/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/isoseq/refine/blobs/sha256:bcd5a901b93ff78ca99f33e511a0b5cc04582c6ce997008b2f8000f71f3b6860
Size	3.0 KB
Checksum	sha256:bcd5a901b93ff78ca99f33e511a0b5cc04582c6ce997008b2f8000f71f3b6860
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:49:33 (UTC)		1	3.0 KB	-