Added step to run digital normalisation on data
Removed a closing bracket in the wrong place
Do normalisation before error correction, rather than other way around
Wrong variable name fixed
Incorrect hash reference fixed for kmer values
Removed redundant reference to filenames_array
Imported File::Copy into pool_fastq.pl script
Use default filename from khmer. Also added quotes around filename for error correction
Removed GzipError import
Added missing /
Corrected paths to normalised and corrected fastq files in pool_fastqs
Corrected minor typos in pool_fastqs.pl
Sort the file names in pool fastqs
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_subsampling_to_pipeline

Conflicts:
	modules/VertRes/Pipelines/Assembly.pm
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_subsampling_to_pipeline
Merge branch 'pipeline' into add_sga_step_to_pipeline
Merge branch 'add_sga_step_to_pipeline' into add_subsampling_to_pipeline

Conflicts:
	modules/VertRes/Pipelines/Assembly.pm
Error correction and normalisation steps in pool fastqs updated, and now touch a done file after completion
Minor edit to comment regarding calculating kmer sizes
Changed pe_mode from 1 to 2