modules/htslib_bgziptabix

Multi-purpose module to compress, decompress and index files using bgzip and tabix.

compressdecompressindexbgziptabixgzipbzipxz

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

Description

Multi-purpose module to compress, decompress and index files using bgzip and tabix.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘sample1’ ]

`infile`
`:file`

Input file to compress or decompress

*

`infile_tbi`
`:file`

Optional tabix index for the input file.

*.{tbi,csi}

`regions`
`:file`

Optional file of regions to extract (BED or chr:start-end format). Only used when creating an index for the output file.

*.{bed,txt,tsv}

`action`
`:string`

Action to perform, either compress or decompress

`make_index`
`:boolean`

Whether to create a tabix index for the output file; only used if action is compress

`out_ext`
`:string`

Output file extension without .gz suffix (for example vcf)

Output

name:type

description

pattern

`output`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘sample1’ ]

`${outfile}`
`:file`

Compressed or decompressed output file

*

`index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘sample1’ ]

`${outfile}.{tbi,csi}`
`:file`

Tabix index file for the compressed output file

*.{tbi,csi}

`versions_htslib`

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

The name of the process

`htslib`
`:string`

The name of the tool

`bgzip --version | sed '1! d; s/bgzip (htslib) //'`
`:eval`

The expression to obtain the version of the tool

`versions_xz`

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

The name of the process

`xz`
`:string`

The name of the tool

`xz --version | sed '1! d; s/xz (XZ Utils) //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`htslib`
`:string`

The name of the tool

`bgzip --version | sed '1! d; s/bgzip (htslib) //'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`xz`
`:string`

The name of the tool

`xz --version | sed '1! d; s/xz (XZ Utils) //'`
`:eval`

The expression to obtain the version of the tool

Tools

htslib
MIT

C library for high-throughput sequencing data formats.

http://www.htslib.org http://www.htslib.org/doc https://github.com/samtools/htslib 10.1093/gigascience/giab007

modules/htslib_bgziptabix

Description

Input

`meta`
`:map`

`infile`
`:file`

`infile_tbi`
`:file`

`regions`
`:file`

`action`
`:string`

`make_index`
`:boolean`

`out_ext`
`:string`

Output

`output`

`meta`
`:map`

`${outfile}`
`:file`

`index`

`meta`
`:map`

`${outfile}.{tbi,csi}`
`:file`

`versions_htslib`

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

`htslib`
`:string`

`bgzip --version | sed '1! d; s/bgzip (htslib) //'`
`:eval`

`versions_xz`

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

`xz`
`:string`

`xz --version | sed '1! d; s/xz (XZ Utils) //'`
`:eval`

Topics

`versions`

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

`htslib`
`:string`

`bgzip --version | sed '1! d; s/bgzip (htslib) //'`
`:eval`

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

`xz`
`:string`

`xz --version | sed '1! d; s/xz (XZ Utils) //'`
`:eval`

Tools

htslib
MIT

maintainer

get in touch

modules/htslib_bgziptabix

Description

Input

meta:map

infile:file

infile_tbi:file

regions:file

action:string

make_index:boolean

out_ext:string

Output

output

meta:map

${outfile}:file

index

meta:map

${outfile}.{tbi,csi}:file

versions_htslib

${task.process}:string

htslib:string

bgzip --version | sed '1! d; s/bgzip (htslib) //':eval

versions_xz

${task.process}:string

xz:string

xz --version | sed '1! d; s/xz (XZ Utils) //':eval

Topics

versions

${task.process}:string

htslib:string

bgzip --version | sed '1! d; s/bgzip (htslib) //':eval

${task.process}:string

xz:string

xz --version | sed '1! d; s/xz (XZ Utils) //':eval

Tools

htslib MIT

maintainer

get in touch

`meta`
`:map`

`infile`
`:file`

`infile_tbi`
`:file`

`regions`
`:file`

`action`
`:string`

`make_index`
`:boolean`

`out_ext`
`:string`

`output`

`meta`
`:map`

`${outfile}`
`:file`

`index`

`meta`
`:map`

`${outfile}.{tbi,csi}`
`:file`

`versions_htslib`

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

`htslib`
`:string`

`bgzip --version | sed '1! d; s/bgzip (htslib) //'`
`:eval`

`versions_xz`

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

`xz`
`:string`

`xz --version | sed '1! d; s/xz (XZ Utils) //'`
`:eval`

`versions`

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

`htslib`
`:string`

`bgzip --version | sed '1! d; s/bgzip (htslib) //'`
`:eval`

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

`xz`
`:string`

`xz --version | sed '1! d; s/xz (XZ Utils) //'`
`:eval`

htslib
MIT