Align fastq files to a reference genome
meta :map
Groovy Map containing sample information e.g. [ id:‘test’ ]
reads :file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2 :map
Groovy Map containing reference information e.g. [ id:‘test’ ]
index :file
Aligner genome index files
Directory containing aligner index
meta3 :map
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta :file
Reference genome in fasta format
*.{fa, fasta, fna}
aligner :string
Aligner to use for alignment
sort_bam :boolean
sort output
bam :file
BAM file
*.bam
bam_index :file
BAM index (currently only for snapaligner)
*.{bai, csi}
report :file
Alignment report (currently only for dragmap)
*.txt
versions :file
File containing software versions
versions.yml
