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}

meta2:map

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

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}

fai

meta:map

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

*.fai:file

FASTA index file

*.{fai}

sizes

meta:map

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

*.sizes:file

File containing chromosome lengths

*.{sizes}

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

versions.yml:file

File containing software versions

versions.yml

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
bamtofastq callingcards circdna circrna createpanelrefs cutandrun fastquorum mag methylong methylseq nanoseq oncoanalyser pangenome pathogensurveillance phaseimpute radseq raredisease references rnadnavar rnafusion rnavar sammyseq sarek scnanoseq tfactivity
Github user maxulysse
Github user phue
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