modules/smoove_call

smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.

structural variantsSVvcfwgs

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file

*.{bam,cram}

`index`
`:file`

Index of BAM/CRAM file

*.{bai,crai}

`exclude_beds`
`:file`

A BED file containing the regions to exclude from the SV calling

*.bed

`meta2`
`:map`

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

`fasta`
`:file`

The reference fasta file

*.{fasta,fna,fa}

`meta3`
`:map`

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

`fai`
`:file`

Index of reference fasta file

*.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

`versions_smoove`

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

The name of the process

`smoove`
`:string`

The name of the tool

`smoove -v |& sed -n 's/smoove version: *//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

`smoove`
`:string`

The name of the tool

`smoove -v |& sed -n 's/smoove version: *//p'`
`:eval`

The expression to obtain the version of the tool

Tools

smoove
Apache-2.0

structural variant calling and genotyping with existing tools, but, smoothly

github.com/brentp/smoove brentp.github.io/post/smoove https://github.com/brentp/smoove

modules/smoove_call

Description

Input

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`exclude_beds`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`versions_smoove`

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

`smoove`
`:string`

`smoove -v |& sed -n 's/smoove version: *//p'`
`:eval`

Topics

`versions`

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

`smoove`
`:string`

`smoove -v |& sed -n 's/smoove version: *//p'`
`:eval`

Tools

smoove
Apache-2.0

maintainers

get in touch

modules/smoove_call

Description

Input

meta:map

input:file

index:file

exclude_beds:file

meta2:map

fasta:file

meta3:map

fai:file

Output

vcf

meta:map

*.vcf.gz:file

versions_smoove

${task.process}:string

smoove:string

smoove -v |& sed -n 's/smoove version: *//p':eval

Topics

versions

${task.process}:string

smoove:string

smoove -v |& sed -n 's/smoove version: *//p':eval

Tools

smoove Apache-2.0

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`exclude_beds`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`versions_smoove`

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

`smoove`
`:string`

`smoove -v |& sed -n 's/smoove version: *//p'`
`:eval`

`versions`

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

`smoove`
`:string`

`smoove -v |& sed -n 's/smoove version: *//p'`
`:eval`

smoove
Apache-2.0