modules/tabix_bgziptabix

DEPRECATED. Use HTSLIB/BGZIPTABIX instead. bgzip a sorted tab-delimited genome file and then create tabix index

bgzipcompressindextabixvcf

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

Description

DEPRECATED. Use HTSLIB/BGZIPTABIX instead. bgzip a sorted tab-delimited genome file and then create tabix index

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

Sorted tab-delimited genome file

Output

name:type

description

pattern

`gz_index`

`meta`
`:map`

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

`*.gz`
`:file`

bgzipped tab-delimited genome file

*.gz

`*.{tbi,csi}`
`:file`

Tabix index file (either tbi or csi)

*.{tbi,csi}

`versions_tabix`

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

The process the versions were collected from

`tabix`
`:string`

The tool name

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

The expression to obtain the version of the tool

`versions_bgzip`

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

The process the versions were collected from

`bgzip`
`:string`

The tool name

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`tabix`
`:string`

The tool name

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

The expression to obtain the version of the tool

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

The process the versions were collected from

`bgzip`
`:string`

The tool name

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

tabix
MIT

Generic indexer for TAB-delimited genome position files.

htslib.org/doc/tabix htslib.org/doc/tabix.1 10.1093/bioinformatics/btq671

modules/tabix_bgziptabix

Description

Input

`meta`
`:map`

`input`
`:file`

Output

`gz_index`

`meta`
`:map`

`*.gz`
`:file`

`*.{tbi,csi}`
`:file`

`versions_tabix`

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

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

`versions_bgzip`

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

`bgzip`
`:string`

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

Topics

`versions`

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

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

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

`bgzip`
`:string`

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

Tools

tabix
MIT

included in

maintainers

get in touch

modules/tabix_bgziptabix

Description

Input

meta:map

input:file

Output

gz_index

meta:map

*.gz:file

*.{tbi,csi}:file

versions_tabix

${task.process}:string

tabix:string

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':eval

versions_bgzip

${task.process}:string

bgzip:string

bgzip --version | sed '1!d;s/.* //':eval

Topics

versions

${task.process}:string

tabix:string

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':eval

${task.process}:string

bgzip:string

bgzip --version | sed '1!d;s/.* //':eval

Tools

tabix MIT

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`gz_index`

`meta`
`:map`

`*.gz`
`:file`

`*.{tbi,csi}`
`:file`

`versions_tabix`

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

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

`versions_bgzip`

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

`bgzip`
`:string`

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

`versions`

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

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

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

`bgzip`
`:string`

`bgzip --version | sed '1!d;s/.* //'`
`:eval`

tabix
MIT