Test commit
Added code to run SGA error correction in assembly pipeline if SGA parameter is set
Added error correction option to pool fastqs
Syntax errors corrected
Increased memory for pool fastqs
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_sga_step_to_pipeline
Syntax errors fixed in pool fastqs perl script
Provide full paths to the fastq files in pool_fastqs
Construct full  paths for the fastq files before sending them for error correction
Added a missing semi colon
Undeclared variables fixed
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_sga_step_to_pipeline
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_sga_step_to_pipeline
Merge branch 'pipeline' into add_sga_step_to_pipeline

Conflicts:
	modules/VertRes/Pipelines/Assembly.pm
Merge pull request #203 from nds/add_sga_step_to_pipeline

Add sga step to pipeline