Nextflow Registry | nf-core/abyss/abysspe@0.0.0-0c7146d

nf-core/abyss/abysspe @ 0.0.0-0c7146d

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @LiaOb21

Maintainers: @LiaOb21

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

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

include { ABYSS_ABYSSPE } from 'nf-core/abyss/abysspe'

MIT License

Process

`Name`	`ABYSS_ABYSSPE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`reads` file	List of input paired-end FastQ files (R1 and R2). Must be paired-end reads; ABySS requires paired reads for assembly. `*.{fastq.gz,fastq,fq.gz,fq}`
`merged` file	Optional merged/overlapping paired-end reads or supplementary single-end reads. Use empty list `[]` if not available. `*.{fastq.gz,fastq,fq.gz,fq}`

`kmersize` integer	K-mer size for assembly. Must be an odd number.

Output 5 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*-abyss.log` file	ABySS assembly log file `*-abyss.log`

#2 stats tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*-stats` file	Assembly statistics file `*-stats`

#3 contigs tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*-contigs.fa.gz` file	Assembled contigs in FASTA format `*-contigs.fa.gz`

#4 scaffolds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*-scaffolds.fa.gz` file	Assembled scaffolds in FASTA format `*-scaffolds.fa.gz`

#5 versions_abyss tuple

`${task.process}` string	The name of the process
`abyss` string	The name of the tool
`abyss-pe version \| grep abyss \| cut -d" " -f3` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
abyss	Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.	https://github.com/bcgsc/abyss/blob/v2.3.10/README.md

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:20:57 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fabyss%2Fabysspe/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/abyss/abysspe/blobs/sha256:976ccf31ce753517785a478cd3b8c5b6f0a0b339505aa32d31e83b52161c08c4
Size	3.2 KB
Checksum	sha256:976ccf31ce753517785a478cd3b8c5b6f0a0b339505aa32d31e83b52161c08c4
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:20:57 (UTC)		1	3.2 KB	-