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