[module1]

;;path to speedseq package binary directory
$;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/
;;Sequence file 1
$;Seq1File$; = "[% seq1 %]"
;;Sequence file 2
$;Seq2File$; = "[% seq2 %]"
;;Read Group
$;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\tPU:NA12878'
;;Reference
$;Reference$; = "[% ref %]"

[module2]

 ;;Output Chromosome
 $;Chromosome$; = "[% chr_list %]"
 ;;use --v for verbose summary
 $;OTHER_ARGS$; = --v