fasta_index_dna

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

fastaindexbowtie2bwamembwamem2dragmapsnapaligner

Description

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

name

description

pattern

Reference genome fasta file.

Structure: [ val(meta), path(fasta) ]

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

Structure: [ val(meta2), path(altliftover) ]

Aligner to use for alignment

name

description

pattern

Aligner index.

Structure: [ val(meta), path(index) ]