Create a SNAP index for reference genome
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
Input genome fasta file
altcontigfile{:bash}
Optional file with a list of alt contig names, one per line.
nonaltcontigfile{:bash}
Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
altliftoverfile{:bash}
Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
index{:bash}
SNAP genome index files
{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}
snap/*{:bash}
versions_snapaligner{:bash}
${task.process}{:bash}
:string
The name of the process
snap-aligner{:bash}
The name of the tool
snap-aligner 2>&1 | sed 's/^.*version //;s/.\$//;q'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
