Do not need to use -d option as we use the ropebwt indexing algorithm
Accept one interleaved fastq file
Adjust parameters to reflect the preprocessing of one fastq file, default algorith ropebwt and no -d disk value
Test if SGA code can handle a single interleaved fastq file
Edited to handle a single interleaved fastq file in addition to separate forward and reverse files
Corrected wrong variable name and added missing brackets.
Fixed extra brackets
Only move the results file if it exists
Do not zip SGA corrected file by default
Minor change to comments
Minor changes to getting the cwd at start of script
Merge pull request #20 from nds/add_sga_step

Add sga step