Align fastq files to a reference genome
meta
Groovy Map containing sample information e.g. [ id:‘test’ ]
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2
Groovy Map containing reference information e.g. [ id:‘test’ ]
index
Aligner genome index files
Directory containing aligner index
aligner
Aligner to use for alignment
sort_bam
sort output
bam
BAM file
*.bam
bai
BAM index (currently only for snapaligner)
*.bai
report
Alignment report (currently only for dragmap)
*.txt
versions
File containing software versions
versions.yml
