Description

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 ]

${prefix}.*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
included in
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maintainers
Github user joseespinosa
Github user drpatelh
Github user maxulysse
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