Description

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

Input

name:type
description
pattern

meta :map

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

fasta :file

Reference genome fasta file

meta2 :map

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

altliftover :file

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 :string

Aligner to use for alignment

Output

name:type
description
pattern

meta :map

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

index :file

aligner index

versions :file

File containing software versions

versions.yml
included modules and subworkflows
bowtie2/build bwa/index bwamem2/index dragmap/hashtable snapaligner/index
maintainers
Github user matthdsm
Github user ramprasadn
get in touch
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