modules/paragraph_vcf2paragraph

Convert a VCF file to a JSON graph

vcfjsonstructural_variants

https://github.com/nf-core/modules/[...]/modules/nf-core/paragraph/vcf2paragraph

Description

Convert a VCF file to a JSON graph

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

The VCF/BCF file

*.{vcf,bcf}(.gz)?

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`fasta`
`:file`

Reference genome VCF was generated against

*.{fasta,fna,fa}

Output

name:type

description

pattern

`graph`

`meta`
`:map`

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

`*.json.gz`
`:file`

The created graph in BGZIP format

*.json.gz

`versions_paragraph`

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

The name of the process

`paragraph`
`:string`

The name of the tool

`2.3`
`:string`

The expression to obtain the version of the tool

`versions_bgzip`

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

The name of the process

`bgzip`
`:string`

The name of the tool

`bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.Version: //; s/ .\$//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`paragraph`
`:string`

The name of the tool

`2.3`
`:string`

The expression to obtain the version of the tool

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

The name of the process

`bgzip`
`:string`

The name of the tool

`bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.Version: //; s/ .\$//'`
`:eval`

The expression to obtain the version of the tool

Tools

paragraph
Apache License 2.0

Graph realignment tools for structural variants

github.com/Illumina/paragraph 10.1101/635011

modules/paragraph_vcf2paragraph

Description

Input

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`fasta`
`:file`

Output

`graph`

`meta`
`:map`

`*.json.gz`
`:file`

`versions_paragraph`

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

`paragraph`
`:string`

`2.3`
`:string`

`versions_bgzip`

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

`bgzip`
`:string`

`bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.Version: //; s/ .\$//'`
`:eval`

Topics

`versions`

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

`paragraph`
`:string`

`2.3`
`:string`

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

`bgzip`
`:string`

`bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.Version: //; s/ .\$//'`
`:eval`

Tools

paragraph
Apache License 2.0

maintainer

get in touch

modules/paragraph_vcf2paragraph

Description

Input

meta :map

vcf :file

meta2 :map

fasta :file

Output

graph

meta :map

*.json.gz :file

versions_paragraph

${task.process} :string

paragraph :string

2.3 :string

versions_bgzip

${task.process} :string

bgzip :string

bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.*Version: //; s/ .*\$//' :eval

Topics

versions

${task.process} :string

paragraph :string

2.3 :string

${task.process} :string

bgzip :string

bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.*Version: //; s/ .*\$//' :eval

Tools

paragraphApache License 2.0

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`graph`

`meta`
`:map`

`*.json.gz`
`:file`

`versions_paragraph`

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

`paragraph`
`:string`

`2.3`
`:string`

`versions_bgzip`

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

`bgzip`
`:string`

`bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.Version: //; s/ .\$//'`
`:eval`

`versions`

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

`paragraph`
`:string`

`2.3`
`:string`

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

`bgzip`
`:string`

`bgzip -h 2>&1 | tr ' ' ' ' | sed 's/^.Version: //; s/ .\$//'`
`:eval`

paragraph
Apache License 2.0