Nextflow Registry | nf-core/braker3@0.0.0-7f68141

nf-core/braker3 @ 0.0.0-7f68141

Gene prediction in novel genomes using RNA-seq and protein homology information

genome annotation braker gff gtf

Latest version: 0.0.0-7f68141

Total downloads: 7

Source: nf-core/modules

Authors: @kherronism @GallVp

Maintainers: @GallVp

Gene prediction in novel genomes using RNA-seq and protein homology information

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

include { BRAKER3 } from 'nf-core/braker3'

MIT License

Process

`Name`	`BRAKER3`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`fasta` file	Genome assembly fasta `*.{fasta,fa,fas,faa,fna}`

`bam` file	BAM file of RNA-seq data to be passed to --bam `*.bam`

`rnaseq_sets_dirs` file	Directories of RNA-seq data sets to be passed to --rnaseq_sets_dirs

`rnaseq_sets_ids` file	IDs of RNA-seq data sets to be passed to --rnaseq_sets_ids

`proteins` file	Protein evidence to be passed to --proteins `*.{fasta,fa,fas,faa}`

`hintsfile` file	Hintsfile to be passed to --hintsfile `*.{gff, gtf, gff3}`

Output 11 channels

#1 aa tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/braker.aa` file	Protein sequence file as output by BRAKER3 `*.{aa}`

#2 cds tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/braker.codingseq` file	Coding sequence file as output by BRAKER3 `*.{codingseq}`

#3 gtf tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/braker.gtf` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`

#4 log tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/braker.log` file	BRAKER3 log file `*.log`

#5 gff3 tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/braker.gff3` file	GFF3 file as output by BRAKER3 `*.{gff3}`

#6 citations tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/what-to-cite.txt` file	BRAKER3 citations `what-to-cite.txt`

#7 hintsfile tuple

`meta` file	Gene transfer format file as output by BRAKER3 `*.{gtf}`
`$prefix/hintsfile.gff` file	Hints file as output by BRAKER3 `*hintsfile.{gff}`

#8 versions_braker3 tuple

`${task.process}` string	The name of the process
`braker3` string	The name of the tool
`braker.pl --version 2>/dev/null \| sed 's/braker.pl version //'` eval	The expression to obtain the version of the tool

#9 versions_augustus tuple

`${task.process}` string <