Create a SNAP index for reference genome
meta2
Groovy Map containing reference information e.g. [ id:‘test’, single_end
fasta
Input genome fasta file
altcontigfile
Optional file with a list of alt contig names, one per line.
nonaltcontigfile
Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
altliftoverfile
Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
index
SNAP genome index files
{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}
versions
File containing software versions
versions.yml
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
