modules/annotsv_annotsv

Annotation and Ranking of Structural Variation

annotationstructural variantsvcfbedtsv

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

Description

Annotation and Ranking of Structural Variation

Input

name:type

description

pattern

`meta`
`:map`

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

`sv_vcf`
`:file`

A VCF or BED file containing the structural variants to be annotated

*.{bed,vcf,vcf.gz}

`sv_vcf_index`
`:file`

OPTIONAL - The index for gzipped VCF files

*.tbi

`candidate_small_variants`
`:file`

OPTIONAL - A file containing candidate small variants

*.{vcf,vcf.gz}

`meta2`
`:map`

Groovy Map containing annotations information

`annotations`
`:directory`

The directory containing the annotations (URL to download this will be made available soon) For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)

`meta3`
`:map`

Groovy Map containing candidate genes information

`candidate_genes`
`:file`

OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)

*.txt

`meta4`
`:map`

Groovy Map containing candidate false positive SNV information

`false_positive_snv`
`:file`

OPTIONAL - A VCF file containing small variant candidates

*.{vcf,vcf.gz}

`meta5`
`:map`

Groovy Map containing candidate gene transcripts information

`gene_transcripts`
`:file`

OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)

*.txt

Output

name:type

description

pattern

`tsv`

`meta`
`:map`

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

`*.tsv`
`:file`

A TSV file containing the annotated variants

*.tsv

`unannotated_tsv`

`meta`
`:map`

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

`*.unannotated.tsv`
`:file`

OPTIONAL - TSV file containing the unannotated variants

*.unannotated.tsv

`vcf`

`meta`
`:map`

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

`*.vcf`
`:file`

OPTIONAL - A VCF file containing the annotated variants (created when -vcf 1 is specified in the args)

*.vcf

`versions_annotsv`

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

The name of the process

`annotsv`
`:string`

The name of the tool

`AnnotSV --version | sed 's/AnnotSV //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`annotsv`
`:string`

The name of the tool

`AnnotSV --version | sed 's/AnnotSV //'`
`:eval`

The expression to obtain the version of the tool

Tools

annotsv
GPL-3.0

Annotation and Ranking of Structural Variation

lbgi.fr/AnnotSV https://github.com/lgmgeo/AnnotSV 10.1093/bioinformatics/bty304

modules/annotsv_annotsv

Description

Input

`meta`
`:map`

`sv_vcf`
`:file`

`sv_vcf_index`
`:file`

`candidate_small_variants`
`:file`

`meta2`
`:map`

`annotations`
`:directory`

`meta3`
`:map`

`candidate_genes`
`:file`

`meta4`
`:map`

`false_positive_snv`
`:file`

`meta5`
`:map`

`gene_transcripts`
`:file`

Output

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`unannotated_tsv`

`meta`
`:map`

`*.unannotated.tsv`
`:file`

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_annotsv`

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

`annotsv`
`:string`

`AnnotSV --version | sed 's/AnnotSV //'`
`:eval`

Topics

`versions`

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

`annotsv`
`:string`

`AnnotSV --version | sed 's/AnnotSV //'`
`:eval`

Tools

annotsv
GPL-3.0

included in

maintainer

get in touch

modules/annotsv_annotsv

Description

Input

meta:map

sv_vcf:file

sv_vcf_index:file

candidate_small_variants:file

meta2:map

annotations:directory

meta3:map

candidate_genes:file

meta4:map

false_positive_snv:file

meta5:map

gene_transcripts:file

Output

tsv

meta:map

*.tsv:file

unannotated_tsv

meta:map

*.unannotated.tsv:file

vcf

meta:map

*.vcf:file

versions_annotsv

${task.process}:string

annotsv:string

AnnotSV --version | sed 's/AnnotSV //':eval

Topics

versions

${task.process}:string

annotsv:string

AnnotSV --version | sed 's/AnnotSV //':eval

Tools

annotsv GPL-3.0

included in

maintainer

get in touch

`meta`
`:map`

`sv_vcf`
`:file`

`sv_vcf_index`
`:file`

`candidate_small_variants`
`:file`

`meta2`
`:map`

`annotations`
`:directory`

`meta3`
`:map`

`candidate_genes`
`:file`

`meta4`
`:map`

`false_positive_snv`
`:file`

`meta5`
`:map`

`gene_transcripts`
`:file`

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`unannotated_tsv`

`meta`
`:map`

`*.unannotated.tsv`
`:file`

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_annotsv`

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

`annotsv`
`:string`

`AnnotSV --version | sed 's/AnnotSV //'`
`:eval`

`versions`

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

`annotsv`
`:string`

`AnnotSV --version | sed 's/AnnotSV //'`
`:eval`

annotsv
GPL-3.0