Performs fastq alignment to a fasta reference using SNAP
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
*.{fastq.gz,fq.gz,fastq,fq,bam}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]
index{:bash}
List of SNAP genome index files
{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}
bam{:bash}
*.bam{:bash}
Aligned BAM file
*.{bam}
bai{:bash}
*.bai{:bash}
Optional aligned BAM file index
*.{bai}
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
