modules/survivor_merge

Compare or merge VCF files to generate a consensus or multi sample VCF files.

survivormergevcfstructural variants

https://github.com/nf-core/modules/[...]/modules/nf-core/survivor/merge

Description

Compare or merge VCF files to generate a consensus or multi sample VCF files.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`vcfs`
`:list`

The VCF files to be merged Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158

*.vcf

`max_distance_breakpoints`
`:integer`

Max distance between breakpoints (0-1 percent of length, 1- number of bp)

`min_supporting_callers`
`:integer`

Minimum number of supporting caller

`account_for_type`
`:integer`

Take the type into account (1==yes, else no)

`account_for_sv_strands`
`:integer`

Take the strands of SVs into account (1==yes, else no)

`estimate_distanced_by_sv_size`
`:integer`

Estimate distance based on the size of SV (1==yes, else no)

`min_sv_size`
`:integer`

Minimum size of SVs to be taken into account

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.vcf`
`:file`

The merged VCF file

*.vcf

`versions_survivor`

`${task.process}`
`:string`

The process the versions were collected from

`survivor`
`:string`

The name of the tool

`SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`survivor`
`:string`

The name of the tool

`SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'`
`:eval`

The expression to obtain the version of the tool

Tools

survivor
MIT

Toolset for SV simulation, comparison and filtering

github.com/fritzsedlazeck/SURVIVOR/wiki https://github.com/fritzsedlazeck/SURVIVOR 10.1038/NCOMMS14061

modules/survivor_merge

Description

Input

`meta`
`:map`

`vcfs`
`:list`

`max_distance_breakpoints`
`:integer`

`min_supporting_callers`
`:integer`

`account_for_type`
`:integer`

`account_for_sv_strands`
`:integer`

`estimate_distanced_by_sv_size`
`:integer`

`min_sv_size`
`:integer`

Output

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_survivor`

`${task.process}`
`:string`

`survivor`
`:string`

`SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`survivor`
`:string`

`SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'`
`:eval`

Tools

survivor
MIT

included in

maintainer

get in touch

modules/survivor_merge

Description

Input

meta:map

vcfs:list

max_distance_breakpoints:integer

min_supporting_callers:integer

account_for_type:integer

account_for_sv_strands:integer

estimate_distanced_by_sv_size:integer

min_sv_size:integer

Output

vcf

meta:map

*.vcf:file

versions_survivor

${task.process}:string

survivor:string

SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //':eval

Topics

versions

${task.process}:string

survivor:string

SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //':eval

Tools

survivor MIT

included in

maintainer

get in touch

`meta`
`:map`

`vcfs`
`:list`

`max_distance_breakpoints`
`:integer`

`min_supporting_callers`
`:integer`

`account_for_type`
`:integer`

`account_for_sv_strands`
`:integer`

`estimate_distanced_by_sv_size`
`:integer`

`min_sv_size`
`:integer`

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_survivor`

`${task.process}`
`:string`

`survivor`
`:string`

`SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'`
`:eval`

`versions`

`${task.process}`
`:string`

`survivor`
`:string`

`SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'`
`:eval`

survivor
MIT