broadinstitute/picard — pull request #13 by nnordborg (2014-05-28 07:14:23+00:00)
Title: Compress outputs in IlluminaBasecallsToFastq

I have added COMPRESS_OUTPUTS command line parameter to IlluminaBasecallsToFastq so that it can generate compressed FASTQ files (with file extension .fastq.gz). This saves temporary disk space and the need for a separate compression step. Hope this is useful for someone else as well and that it can be merged to the master Picard branch.

/Nicklas