Generate index files from reference fasta for bismark and bwameth
fasta_fai
Reference genome Structure: [ val(meta), path(fasta), path(fai) ]
*.{fa/fa.gz,fai}
bismark_index
Bismark genome index files Structure: [ val(meta), path(bismark_index) ]
bwameth_index
Bwameth genome index files Structure: [ val(meta), path(bwameth_index) ]
aligner
Aligner name (bismark, bismark_hisat, or bwameth)
use_mem2
Build a mem2 index when bwameth is chosen as an aligner, and an index path is not supplied
Reference genome and its index
Structure: [ val(meta), path(fasta), path(fai) ]
*.{fa,fai}
Bismark genome index files
Structure: [ val(meta), path(bismark_index) ]
BismarkIndex
Bwameth genome index files
Structure: [ val(meta), path(bwameth_index) ]
index
