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

nf-core/pilon @ 0.0.0-6c4ed3a

Automatically improve draft assemblies and find variation among strains, including large event detection

polishing assembly variant calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @scorreard

Maintainers: @scorreard

Summary

Automatically improve draft assemblies and find variation among strains, including large event detection

Get started

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

include { PILON } from 'nf-core/pilon'

License

MIT License

Process

`Name`	`PILON`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information for the fasta e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA of the input genome `*.{fasta}`

#2 tuple

`meta2` map	Groovy Map containing sample information for the bam file e.g. [ id:'test', single_end:false ]
`bam` file	BAM file of reads aligned to the input genome `*.{bam}`
`bai` file	BAI file (BAM index) of BAM reads aligned to the input genome `*.{bai}`

`pilon_mode` string	Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).

pilon_mode string

Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).

Output 6 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf` file	Pilon variant output `*.{vcf}`

#2 tracks_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed` file	files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats `*.{bed}`

#3 tracks_wig tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.wig` file	files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats `*.{wig}`

#4 change_record tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.change` file	file containing a space-delimited record of every change made in the assembly as instructed by the --fix option `*.{change}`

#5 versions_pilon tuple

`${task.process}` string	The name of the process
`pilon` string	The name of the tool
`pilon --version \| sed 's/^.version //; s/ .\$//'` eval	The expression to obtain the version of the tool

#6 improved_assembly tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fasta` file	fasta file, improved assembly `*.{fasta}`

Tool	Description	Homepage
pilon	Pilon is an automated genome assembly improvement and variant detection tool.	https://github.com/broadinstitute/pilon/wiki

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:36:28 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpilon/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pilon/blobs/sha256:cdc6bedc286fc0b29af73d35c54b7e5fd9c08eaa493fdb86b0842e02815ccbc9
Size	3.5 KB