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Added the shallow input to enable shallow mode. Defaults to false.
Added the runPolyGTrimming input to control whether or not poly-
G-tail trimming should be performed by fastp. By default fastp's
default behaviour will be used, ie. enabled for NextSeq/NovaSeq data
as determined from the FastQ headers.
Added the mappingThreads input to control the number of threads
used per BWA mem job. Defaults to 8.
Added the splitFastq input to control whether fastq files should
get split into chunks or not. Defaults to true.
Added the filterFastq input to control whether fastq files should
get filtered on quality and read length prior to mapping. Default to
true.
Added the fastpCorrection input to control whether fastp's
correction should be enabled. DEfaults to true.