Nextflow Registry | nf-core/rseqc/junctionannotation@0.0.0-6c4ed3a

nf-core/rseqc/junctionannotation @ 0.0.0-6c4ed3a

compare detected splice junctions to reference gene model

junctions splicing rnaseq

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @drpatelh @kevinmenden @rhassaine

Maintainers: @drpatelh @kevinmenden @rhassaine

compare detected splice junctions to reference gene model

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

include { RSEQC_JUNCTIONANNOTATION } from 'nf-core/rseqc/junctionannotation'

MIT License

Process

`Name`	`RSEQC_JUNCTIONANNOTATION`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	the alignment in bam format `*.{bam}`
`bai` file	BAM index file `*.{bai}`

`bed` file	a bed file for the reference gene model `*.{bed}`

Output 8 channels

#1 bed tuple

`meta` file	xls file with junction information `*.xls`
`*.junction.bed` file	bed file of annotated junctions `*.junction.bed`

#2 log tuple

`meta` file	xls file with junction information `*.xls`
`*.log` file	Log file of execution `*.junction_annotation.log`

#3 pdf tuple

`meta` file	xls file with junction information `*.xls`
`*junction.pdf` file	junction plot `*.junction.pdf`

#4 xls tuple

`meta` file	xls file with junction information `*.xls`
`*.xls` file	xls file with junction information `*.xls`

#5 rscript tuple

`meta` file	xls file with junction information `*.xls`
`*.r` file	Rscript to reproduce the plots `*.r`

#6 events_pdf tuple

`meta` file	xls file with junction information `*.xls`
`*events.pdf` file	events plot `*.events.pdf`

#7 interact_bed tuple

`meta` file	xls file with junction information `*.xls`
`*.Interact.bed` file	Interact bed file `*.Interact.bed`

#8 versions_rseqc tuple

`${task.process}` string	The process the versions were collected from
`rseqc` string	The tool name
`junction_annotation.py --version \| sed "s/junction_annotation.py //"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
rseqc	RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.	http://rseqc.sourceforge.net/