Description

Generate aligner index for a reference genome. Please note, this workflow requires input CHANNELS. Input values will cause errors

Input

name
description
pattern

meta

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

fasta

Reference genome fasta file

meta2

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

altliftover

Sam formatted liftover file for the reference genome alt contigs
See: https://github.com/lh3/bwa/blob/master/README-alt.md
Download from: https://sourceforge.net/projects/bio-bwa/files/bwakit

val_aligner

Aligner to use for alignment

Output

name
description
pattern

meta

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

index

aligner index

versions

File containing software versions

versions.yml
bowtie2/build bwa/index bwamem2/index dragmap/hashtable snapaligner/index
Github user matthdsm
Github user ramprasadn
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