Performs fastq alignment to a fasta reference using SNAP
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
: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
Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]
index
List of SNAP genome index files
{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}
bam
*.bam
Aligned BAM file
*.{bam}
bai
*.bai
Optional aligned BAM file index
*.{bai}
versions_snapaligner
${task.process}
:string
The name of the process
snap-aligner
The name of the tool
snap-aligner 2>&1 | sed 's/^.*version //;s/.\$//;q'
:eval
The expression to obtain the version of the tool
versions
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
