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

nf-core/gffcompare @ 0.0.0-6c4ed3a

Compare, merge, annotate and estimate accuracy of generated gtf files

transcripts gtf merge compare

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @jemten

Maintainers: @jemten @gallvp

Compare, merge, annotate and estimate accuracy of generated gtf files

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

include { GFFCOMPARE } from 'nf-core/gffcompare'

MIT License

Process

`Name`	`GFFCOMPARE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`gtfs` file	GTF/GFF files e.g. [ 'file_1.gtf', 'file_2.gtf' ] `*.{gtf,gff}`

#2 tuple

`meta2` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`fasta` file	Genome reference fasta file (optional) `*.{fasta,fa}`
`fai` file	Index for fasta file `*.fai`

#3 tuple

`meta3` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`reference_gtf` file	Reference annotation in gtf/gff format (optional) `*.{gtf,gff}`

Output 8 channels

#1 loci tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.loci` file	File with loci `*.loci`

#2 tmap tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.tmap` file	File listing the most closely matching reference transcript for each query transcript (optional) `*.tmap`

#3 stats tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.stats` file	File with stats for input transcripts as compared to reference alternatively stats for the combined gtf `*.stats`

#4 refmap tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.refmap` file	File listing the reference transcripts with overlapping query transcripts (optional) `*.refmap`

#5 tracking tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.tracking` file	This file matches transcripts up between samples `*.tracking`

#6 combined_gtf tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.combined.gtf` file	Combined gtf file when multiple input files are provided (optional) `*.annotated.gtf`

#7 annotated_gtf tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test', single_end:false ]
`*.annotated.gtf` file	Annotated gtf file when reference gtf is provided (optional) `*.annotated.gtf`

#8 versions_gffcompare tuple

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

Tool	Description	Homepage
gffcompare	GffCompare by Geo Pertea	http://ccb.jhu.edu/software/stringtie/gffcompare.shtml