Description

bgzip a sorted tab-delimited genome file and then create tabix indexes in TBI and CSI format when the coordinate / sequence length is within the supported range of each index format. Compressed files are accepted and will be decompressed on the fly.

Input

Name
Description
Pattern

meta (map)

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

input (file)

Sorted tab-delimited genome file, possibly compressed

max_seq_length (integer)

Maximum length (coordinate) of a sequence in this genome (TSV)

column_numbers (string)

Optional. Columns to extract from the input file, in a format understood by cut e.g. '1-3,5'

header_lines (integer)

Number of header lines to skip from the input file

extension (string)

Extension to name the output file, in case it differs from the input file - for instance, turning a TSV into BED

Output

Name
Description
Pattern

csi

meta (map)

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

*.csi (file)

Tabix index file (CSI format)

*.csi

tbi

meta (map)

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

*.tbi (file)

Tabix index file (TBI format)

*.tbi

gz_index

meta (map)

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

*.gz (file)

bgzipped tab-delimited genome file

*.gz

*.gzi (file)

bgzip index file (GZI format)

*.gzi

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

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
Description
Pattern

versions

${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

${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

bgzip Documentation

Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.

doi: 10.1093/bioinformatics/btp352License: MIT

tabix Documentation

Generic indexer for TAB-delimited genome position files.

doi: 10.1093/bioinformatics/btq671License: MIT
Pipelines with this module
sequencecompositionvariantcallingvariantcomposition
Authors