sample sheet inputs

This release adds the option to use a sample sheet as the input format with each like containing the sample id and the path to input files. Support is also added for running both single and paired reads for the same sample at once.

v1.1.1 fix tmp file permissions bug

Fix tmp file permissions error caused by tmp file attempting to be created at root

v1.1.0 stx2 typing updates

Updates stx2 calling to allow identification of multiple stx2 alleles in a single strain (i.e. stx2a and stx2c in O157:H7).

Note: assemblies will often merge multiple stx2 genes into one assembled gene. Therefore it is only possible to detect multiple stx2 alleles in one strain using raw reads, which allow the frequencies of stx2 type defining SNPs to be evaluated.

Initial release

v1.0.0

update script name