modules/whamg

The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.

whamgwhamvcfbamvariant calling

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/SAM file

*.{bam,sam}

`bai`
`:file`

BAM index file

*.bai

`fasta`
`:file`

Reference Fasta file

*.{fasta,fa}

`fasta_fai`
`:file`

Index of the reference Fasta

*.fai

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

Compressed VCF file

*.vcf.gz

`tbi`

`meta`
`:map`

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

`*.vcf.gz.tbi`
`:file`

Index of the VCF file

*.vcf.gz.tbi

`graph`

`meta`
`:map`

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

`*.txt`
`:file`

Graph file

*.txt

`versions_whamg`

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

The name of the process

`whamg`
`:string`

The name of the tool

`whamg 2>&1 | sed -n 's/^Version: v$[^-]$./\1/p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`whamg`
`:string`

The name of the tool

`whamg 2>&1 | sed -n 's/^Version: v$[^-]$./\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

whamg
MIT

Structural variant detection and association testing

github.com/zeeev/wham 10.1371/journal.pcbi.1004572

modules/whamg

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`graph`

`meta`
`:map`

`*.txt`
`:file`

`versions_whamg`

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

`whamg`
`:string`

`whamg 2>&1 | sed -n 's/^Version: v\([^-]\)./\1/p'`
`:eval`

Topics

`versions`

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

`whamg`
`:string`

`whamg 2>&1 | sed -n 's/^Version: v\([^-]\)./\1/p'`
`:eval`

Tools

whamg
MIT

maintainer

get in touch

modules/whamg

Description

Input

meta:map

bam:file

bai:file

fasta:file

fasta_fai:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.vcf.gz.tbi:file

graph

meta:map

*.txt:file

versions_whamg

${task.process}:string

whamg:string

whamg 2>&1 | sed -n 's/^Version: v\([^-]*\).*/\1/p':eval

Topics

versions

${task.process}:string

whamg:string

whamg 2>&1 | sed -n 's/^Version: v\([^-]*\).*/\1/p':eval

Tools

whamg MIT

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`graph`

`meta`
`:map`

`*.txt`
`:file`

`versions_whamg`

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

`whamg`
`:string`

`whamg 2>&1 | sed -n 's/^Version: v\([^-]\)./\1/p'`
`:eval`

`versions`

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

`whamg`
`:string`

`whamg 2>&1 | sed -n 's/^Version: v\([^-]\)./\1/p'`
`:eval`

whamg
MIT