modules/samtools_faidx

Index FASTA file, and optionally generate a file of chromosome sizes

indexfastafaidxchromosome

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

Description

Index FASTA file, and optionally generate a file of chromosome sizes

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing reference information e.g. [ id:‘test’ ]

`fasta`
`:file`

FASTA file

*.{fa,fasta}

`fai`
`:file`

FASTA index file

*.{fai}

`get_sizes`
`:boolean`

use cut to get the sizes of the index (true) or not (false)

Output

name:type

description

pattern

`fa`

`meta`
`:map`

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

`*.{fa,fasta}`
`:file`

FASTA file

*.{fa}

`sizes`

`meta`
`:map`

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

`*.sizes`
`:file`

File containing chromosome lengths

*.{sizes}

`fai`

`meta`
`:map`

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

`*.fai`
`:file`

FASTA index file

*.{fai}

`gzi`

`meta`
`:map`

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

`*.gzi`
`:file`

Optional gzip index file for compressed inputs

*.gzi

`versions_samtools`

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

The process the versions were collected from

`samtools`
`:string`

The tool name

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

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`samtools`
`:string`

The tool name

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

The command used to generate the version of the tool

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

modules/samtools_faidx

Description

Input

`meta`
`:map`

`fasta`
`:file`

`fai`
`:file`

`get_sizes`
`:boolean`

Output

`fa`

`meta`
`:map`

`*.{fa,fasta}`
`:file`

`sizes`

`meta`
`:map`

`*.sizes`
`:file`

`fai`

`meta`
`:map`

`*.fai`
`:file`

`gzi`

`meta`
`:map`

`*.gzi`
`:file`

`versions_samtools`

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

`samtools`
`:string`

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

Topics

`versions`

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

`samtools`
`:string`

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

Tools

samtools
MIT

included in

maintainers

get in touch

modules/samtools_faidx

Description

Input

meta:map

fasta:file

fai:file

get_sizes:boolean

Output

fa

meta:map

*.{fa,fasta}:file

sizes

meta:map

*.sizes:file

fai

meta:map

*.fai:file

gzi

meta:map

*.gzi:file

versions_samtools

${task.process}:string

samtools:string

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

Topics

versions

${task.process}:string

samtools:string

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

Tools

samtools MIT

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`fai`
`:file`

`get_sizes`
`:boolean`

`fa`

`meta`
`:map`

`*.{fa,fasta}`
`:file`

`sizes`

`meta`
`:map`

`*.sizes`
`:file`

`fai`

`meta`
`:map`

`*.fai`
`:file`

`gzi`

`meta`
`:map`

`*.gzi`
`:file`

`versions_samtools`

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

`samtools`
`:string`

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

`versions`

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

`samtools`
`:string`

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

samtools
MIT