Add output dir option to SRATOOLS_FASTQDUMP_OPTIONS
Add subst statement to make Makefile.halo include from root directory
Multiple updates for new rnaseq pipeline:

1. add FASTQ_SUFFIX variabl
2. rewrite fifo outputs in %.rsem rule
3. update trimmomatic rule
4. add .tmp to tuxedo output directories and mv to output on success
5. added all relevant targets to BROAD_rnaseq