Updated picard to new command syntax

        */

        "picard_markduplicates" {

            args          = "ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"

            args          = "-ASSUME_SORT_ORDER coordinate -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT -TMP_DIR tmp"

            suffix        = ".target.markdup"

            publish_files = false

        }

        }

        "picard_dedup" {

            args          = "ASSUME_SORTED=true REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"

            args          = "-ASSUME_SORT_ORDER coordinate -REMOVE_DUPLICATES true -VALIDATION_STRINGENCY LENIENT -TMP_DIR tmp"

            suffix        = ".target.dedup"

            publish_files = false

        }