modules/tabix_tabix

DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Create a tabix index from a sorted bgzip TAB-delimited genome file, or extract regions from a bgzipped VCF file using an optional regions file.

indextabixvcfextractregions

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

Description

DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Create a tabix index from a sorted bgzip TAB-delimited genome file, or extract regions from a bgzipped VCF file using an optional regions file.

Input

name:type

description

pattern

`meta`
`:map`

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

`tab`
`:file`

TAB-delimited genome position file compressed with bgzip

*.{bed.gz,gff.gz,sam.gz,vcf.gz}

`tai`
`:file`

Tabix index for the input file. Required when extracting regions. Pass [] when creating an index instead.

*.{tbi,csi}

`regions`
`:file`

Optional file of regions to extract (BED or chr:start-end format). Pass [] to create an index instead of extracting regions.

*.{bed,txt,tsv}

Output

name:type

description

pattern

`index`

`meta`
`:map`

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

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

Tabix index file (tbi or csi). Emitted when no regions file is provided.

*.{tbi,csi}

`extracted`

`meta`
`:map`

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

`output.*gz`
`:file`

Bgzipped file of extracted regions, preserving the input file extension. Emitted when a regions file is provided.

*.*gz

`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

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

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_tabix

Description

Input

`meta`
`:map`

`tab`
`:file`

`tai`
`:file`

`regions`
`:file`

Output

`index`

`meta`
`:map`

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

`extracted`

`meta`
`:map`

`output.*gz`
`:file`

`versions_tabix`

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

`tabix`
`:string`

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

Topics

`versions`

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

`tabix`
`:string`

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

Tools

tabix
MIT

included in

maintainers

get in touch

modules/tabix_tabix

Description

Input

meta:map

tab:file

tai:file

regions:file

Output

index

meta:map

*.{tbi,csi}:file

extracted

meta:map

output.*gz:file

versions_tabix

${task.process}:string

tabix:string

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

Topics

versions

${task.process}:string

tabix:string

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

Tools

tabix MIT

included in

maintainers

get in touch

`meta`
`:map`

`tab`
`:file`

`tai`
`:file`

`regions`
`:file`

`index`

`meta`
`:map`

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

`extracted`

`meta`
`:map`

`output.*gz`
`:file`

`versions_tabix`

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

`tabix`
`:string`

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

`versions`

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

`tabix`
`:string`

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

tabix
MIT