modules/vcf2db

A tool to create a Gemini-compatible DB file from an annotated VCF

vcf2dbvcfgemini

https://github.com/nf-core/modules/[...]/modules/nf-core/vcf2db

Description

A tool to create a Gemini-compatible DB file from an annotated VCF

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

VCF file

*.vcf.gz

`ped`
`:file`

PED file

*.ped

Output

name:type

description

pattern

`db`

`meta`
`:map`

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

`*.db`
`:file`

Gemini-compatible database file

*.db

`versions_vcf2db`

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

The name of the process

`vcf2db`
`:string`

The name of the tool

`2020.02.24`
`:string`

The expression to obtain the version of the tool

`versions_python_snappy`

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

The name of the process

`python-snappy`
`:string`

The name of the tool

`0.5.4`
`:string`

The expression to obtain the version of the tool

`versions_snappy`

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

The name of the process

`snappy`
`:string`

The name of the tool

`1.1.8`
`:string`

The expression to obtain the version of the tool

`versions_cyvcf2`

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

The name of the process

`cyvcf2`
`:string`

The name of the tool

`python -c 'import cyvcf2; print(cyvcf2.version)'`
`:eval`

The expression to obtain the version of the tool

`versions_python`

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

The name of the process

`python`
`:string`

The name of the tool

`python --version 2>&1 | awk '{print \$2}'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`vcf2db`
`:string`

The name of the tool

`2020.02.24`
`:string`

The expression to obtain the version of the tool

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

The name of the process

`python-snappy`
`:string`

The name of the tool

`0.5.4`
`:string`

The expression to obtain the version of the tool

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

The name of the process

`snappy`
`:string`

The name of the tool

`1.1.8`
`:string`

The expression to obtain the version of the tool

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

The name of the process

`cyvcf2`
`:string`

The name of the tool

`python -c 'import cyvcf2; print(cyvcf2.version)'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`python`
`:string`

The name of the tool

`python --version 2>&1 | awk '{print \$2}'`
`:eval`

The expression to obtain the version of the tool

Tools

vcf2db
MIT

Create a gemini-compatible database from a VCF

github.com/quinlan-lab/vcf2db

modules/vcf2db

Description

Input

meta:map

vcf:file

ped:file

Output

db

meta:map

*.db:file

versions_vcf2db

${task.process}:string

vcf2db:string

2020.02.24:string

versions_python_snappy

${task.process}:string

python-snappy:string

0.5.4:string

versions_snappy

${task.process}:string

snappy:string

1.1.8:string

versions_cyvcf2

${task.process}:string

cyvcf2:string

python -c 'import cyvcf2; print(cyvcf2.__version__)':eval

versions_python

${task.process}:string

python:string

python --version 2>&1 | awk '{print \$2}':eval

Topics

versions

${task.process}:string

vcf2db:string

2020.02.24:string

${task.process}:string

python-snappy:string

0.5.4:string

${task.process}:string

snappy:string

1.1.8:string

${task.process}:string

cyvcf2:string

python -c 'import cyvcf2; print(cyvcf2.__version__)':eval

${task.process}:string

python:string

python --version 2>&1 | awk '{print \$2}':eval

Tools

vcf2db MIT

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`ped`
`:file`

`db`

`meta`
`:map`

`*.db`
`:file`

`versions_vcf2db`

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

`vcf2db`
`:string`

`2020.02.24`
`:string`

`versions_python_snappy`

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

`python-snappy`
`:string`

`0.5.4`
`:string`

`versions_snappy`

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

`snappy`
`:string`

`1.1.8`
`:string`

`versions_cyvcf2`

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

`cyvcf2`
`:string`

`python -c 'import cyvcf2; print(cyvcf2.version)'`
`:eval`

`versions_python`

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

`python`
`:string`

`python --version 2>&1 | awk '{print \$2}'`
`:eval`

`versions`

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

`vcf2db`
`:string`

`2020.02.24`
`:string`

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

`python-snappy`
`:string`

`0.5.4`
`:string`

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

`snappy`
`:string`

`1.1.8`
`:string`

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

`cyvcf2`
`:string`

`python -c 'import cyvcf2; print(cyvcf2.version)'`
`:eval`

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

`python`
`:string`

`python --version 2>&1 | awk '{print \$2}'`
`:eval`

vcf2db
MIT