Nextflow Registry | nf-core/shovill@0.0.0-6c4ed3a

nf-core/shovill @ 0.0.0-6c4ed3a

Assemble bacterial isolate genomes from Illumina paired-end reads

bacterial assembly illumina

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @rpetit3 @eit-maxlcummins

Maintainers: @rpetit3

Assemble bacterial isolate genomes from Illumina paired-end reads

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

include { SHOVILL } from 'nf-core/shovill'

MIT License

Process

`Name`	`SHOVILL`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input paired-end FastQ files

Output 6 channels

#1 gfa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`contigs.{fastg,gfa,LastGraph}` file	Assembly graph produced by MEGAHIT, SPAdes, or Velvet `contigs.{fastg,gfa,LastGraph}`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`shovill.log` file	Full log file for bug reporting `shovill.log`

#3 contigs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`contigs.fa` file	The final assembly produced by Shovill `contigs.fa`

#4 corrections tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`shovill.corrections` file	List of post-assembly corrections made by Shovill `shovill.corrections`

#5 raw_contigs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`{skesa,spades,megahit,velvet}.fasta` file	Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet) `{skesa,spades,megahit,velvet}.fasta`

#6 versions_shovill tuple

`${task.process}` string	The name of the process
`shovill` string	The name of the tool
`shovill --version 2>&1 \| sed "s/^.*shovill //"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
shovill	Microbial assembly pipeline for Illumina paired-end reads	https://github.com/tseemann/shovill

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:46:07 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fshovill/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/shovill/blobs/sha256:1073af7b018eb3b733216c8573d8187c8b4e39c46120323d4c8f48295c17dc7d
Size	2.9 KB
Checksum	sha256:1073af7b018eb3b733216c8573d8187c8b4e39c46120323d4c8f48295c17dc7d
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:46:07 (UTC)	3	2.9 KB
0.0.0-3fc6d40	22 Apr 2026 15:31:47 (UTC)	3	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:37:53 (UTC)	3