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: 0.0.0-6c4ed3a

Total downloads: 9

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	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:11:09 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fisoseq%2Frefine/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/isoseq/refine/blobs/sha256:1da385157b7fca3e5ad4c9ffd7b4c8373b24714e0bcf8e7426d5189efe920e14
Size	3.0 KB
Checksum	sha256:1da385157b7fca3e5ad4c9ffd7b4c8373b24714e0bcf8e7426d5189efe920e14
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:26:08 (UTC)	3	3.0 KB
0.0.0-3fc6d40	22 Apr 2026 15:18:11 (UTC)	3	3.0 KB
0.0.0-0c7146d	08 Apr 2026 19:11:09 (UTC)	3	3.0 KB