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

nf-core/fusioninspector @ 0.0.0-6c4ed3a

Validation of Fusion Transcript Predictions

fusioninspector fusion RNA-seq fastq

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @rannick @delfiterradas @sofiromano @alanmmobbs93 @martings

Validation of Fusion Transcript Predictions

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

include { FUSIONINSPECTOR } from 'nf-core/fusioninspector'

MIT License

Process

`Name`	`FUSIONINSPECTOR`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	FASTQ file `.{fastq}`
`fusion_list` file	Fusion targets list `*.{txt}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reference` directory	Path to CTAT references `*`

Output 9 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*FusionInspector.log` file	FusionInspector log file `*.log`

#2 tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*FusionInspector.fusions.tsv` file	FusionInspector output TSV file `*.tsv`

#3 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*html` file	HTML output files `*.html`

#4 out_gtf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fi_workdir/*.gtf` file	GTF output file `*.gtf`

#5 versions

`versions.yml` file	File containing software versions `versions.yml`

#6 fi_workdir tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fi_workdir` directory	FusionInspector work directory `fi_workdir`

#7 igv_inputs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`IGV_inputs` directory	IGV inputs directory `IGV_inputs`

#8 chckpts_dir tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`chckpts_dir` directory	Checkpoints directory `chckpts_dir`

#9 abridged_tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*abridged.tsv` file	Abridged TSV output file `*.tsv`

Tool	Description	Homepage
fusioninspector	Validation of Fusion Transcript Predictions	https://github.com/FusionInspector/FusionInspector