modules/pilon

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

polishingassemblyvariant calling

https://github.com/nf-core/modules/[...]/modules/nf-core/pilon

Description

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

Input

name:type

description

pattern

`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}

`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).

Output

name:type

description

pattern

`improved_assembly`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.fasta`
`:file`

fasta file, improved assembly

*.{fasta}

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.vcf`
`:file`

Pilon variant output

*.{vcf}

`change_record`

`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}

`tracks_bed`

`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}

`tracks_wig`

`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}

`versions_pilon`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

pilon
GPL-2.0-or-later

Pilon is an automated genome assembly improvement and variant detection tool.

github.com/broadinstitute/pilon/wiki github.com/broadinstitute/pilon/wiki/Requirements-&-Usage https://github.com/broadinstitute/pilon 10.1371/journal.pone.0112963