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
authors
Github user matthdsm Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub