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

nf-core/flye @ 0.0.0-0c7146d

De novo assembler for single molecule sequencing reads

assembly genome de novo genome assembler single molecule

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @mirpedrol

Maintainers: @mirpedrol

De novo assembler for single molecule sequencing reads

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

include { FLYE } from 'nf-core/flye'

MIT License

Process

`Name`	`FLYE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`reads` file	Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format. `*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}`

`mode` string	Flye mode depending on the input data (source and error rate) `--pacbio-raw\|--pacbio-corr\|--pacbio-hifi\|--nano-raw\|--nano-corr\|--nano-hq`

Output 7 channels

#1 gv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.gv.gz` file	Repeat graph in gv format `*.gv.gz`

#2 gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.gfa.gz` file	Repeat graph in gfa format `*.gfa.gz`

#3 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.log` file	Flye log file `*.log`

#4 txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.txt` file	Extra information and statistics about resulting contigs `*.txt`

#5 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.json` file	Flye parameters `*.json`

#6 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.fasta.gz` file	Assembled FASTA file `*.fasta.gz`

#7 versions_flye tuple

`${task.process}` string	The name of the process
`flye` string	The name of the tool
`flye --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
flye	Fast and accurate de novo assembler for single molecule sequencing reads	https://github.com/fenderglass/Flye

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:39:39 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fflye/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/flye/blobs/sha256:c7488d789e8307594d4835b5d27099f190780c79c84f0593d58097b22ac1e186
Size	3.3 KB
Checksum	sha256:c7488d789e8307594d4835b5d27099f190780c79c84f0593d58097b22ac1e186
Downloads	1

Version