Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

FASTA file

*.{fa,fasta}

meta2{:bash}

:map

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

fai{:bash}

:file

FASTA index file

*.{fai}

get_sizes{:bash}

:boolean

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

Output

name:type
description
pattern

fa{:bash}

meta{:bash}

:map

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

*.{fa,fasta}{:bash}

:file

FASTA file

*.{fa}

sizes{:bash}

meta{:bash}

:map

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

*.sizes{:bash}

:file

File containing chromosome lengths

*.{sizes}

fai{:bash}

meta{:bash}

:map

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

*.fai{:bash}

:file

FASTA index file

*.{fai}

gzi{:bash}

meta{:bash}

:map

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

*.gzi{:bash}

:file

Optional gzip index file for compressed inputs

*.gzi

versions_samtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

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
included in
bamtofastqcallingcardscircdnacircrnacreatepanelrefscutandrunfastquorummagmethylongmethylseqnanoseqoncoanalyserpairgenomealignpangenomepathogensurveillancephaseimputeradseqrarediseasereferencesrnadnavarrnafusionrnavarsammyseqsarekscnanoseqseqinspectortfactivityviralmetagenome
maintainers
Github user maxulysse
Github user phue
get in touch
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