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

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

Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.

gatk4 collectsvevidence structural variants metrics

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Summary

Get started

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

include { GATK4_COLLECTSVEVIDENCE } from 'nf-core/gatk4/collectsvevidence'

License

MIT License

Process

`Name`	`GATK4_COLLECTSVEVIDENCE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`input_index` file	Index of the BAM/CRAM/SAM file `*.{bai,crai,sai}`
`site_depth_vcf` file	Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output `*.vcf.gz`
`site_depth_vcf_tbi` file	Optional - input VCF TBI of SNPs marking loci for site depths, needed for the site depths output `*.vcf.gz.tbi`

`fasta` file	Optional - reference FASTA file needed when the input is a CRAM file `*.{fasta,fa}`

`fasta_fai` file	Optional - index of the reference FASTA file needed when the input is a CRAM file `*.fai`

`dict` file	Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file `*.dict`

Output 7 channels

#1 site_depths tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sd.txt.gz` file	Output file for site depths `*.sd.txt.gz`

#2 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

#3 site_depths_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sd.txt.gz.tbi` file	Index of the output file for site depths `*.sd.txt.gz.tbi`

#4 paired_end_evidence tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pe.txt.gz` file	Output file for paired end evidence `*.pe.txt.gz`

#5 split_read_evidence tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sr.txt.gz` file	Output file for split read evidence `*.sr.txt.gz`

#6 paired_end_evidence_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pe.txt.gz.tbi` file	Index of the output file for paired end evidence `*.pe.txt.gz.tbi`

#7 split_read_evidence_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sr.txt.gz.tbi` file	Index of the output file for split read evidence `*.sr.txt.gz.tbi`

Tool	Description	Homepage
gatk4	Genome Analysis Toolkit (GATK4)	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a