Nextflow Registry | nf-core/gatk4/annotateintervals@0.0.0-6c4ed3a

nf-core/gatk4/annotateintervals @ 0.0.0-6c4ed3a

Annotates intervals with GC content, mappability, and segmental-duplication content

annotateintervals annotation bed gatk4 intervals

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Annotates intervals with GC content, mappability, and segmental-duplication content

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

include { GATK4_ANNOTATEINTERVALS } from 'nf-core/gatk4/annotateintervals'

MIT License

Process

`Name`	`GATK4_ANNOTATEINTERVALS`

Input 8 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`intervals` file	One or more interval files to annotate `*.{interval_list,list,bed}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta` file	The reference FASTA file `*.{fasta,fa}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta_fai` file	The index of the reference FASTA file `*.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'test' ]
`dict` file	The sequence dictionary reference FASTA file `*.dict`

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'test' ]
`mappable_regions` file	Optional - Umap single-read mappability track The track should correspond to the appropriate read length and overlapping intervals must be merged `*.bed(.gz)?`

#6 tuple

`meta6` map	Groovy Map containing reference information e.g. [ id:'test' ]
`mappable_regions_tbi` file	Optional - The index of the gzipped umap single-read mappability track `*.bed.gz.tbi`

#7 tuple

`meta7` map	Groovy Map containing reference information e.g. [ id:'test' ]
`segmental_duplication_regions` file	Optional - Segmental-duplication track `*.bed(.gz)?`

#8 tuple

`meta8` map	Groovy Map containing reference information e.g. [ id:'test' ]
`segmental_duplication_regions_tbi` file	Optional - The index of the gzipped segmental-duplication track `*.bed.gz.tbi`

Output 2 channels

#1 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

#2 annotated_intervals tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tsv` file	The output TSV file with a SAM-style header containing the annotated intervals `*.tsv`

Tool	Description	Homepage
gatk4	Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.	https://gatk.broadinstitute.org/hc/en-us