Align short or PacBio reads to a reference genome using BBMap
Input
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
fastq (file)
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
ref (file)
Either “ref” a directory containing an index, the name of another directory
with a “ref” subdirectory containing an index or the name of a fasta formatted
nucleotide file containg the reference to map to.
Output
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
