Rename contigs after assembly

[elizabethmcd]

This will be a bug later down the road if contig header names after > are not renamed to simplified names such as contig_00001 etc. and remain names that SPAdes gives them

[elizabethmcd]

This only needs to be done for metaspades since flye outputs sensible contig names. Unless want to append assemblyname_contig_01 for example or have a good amount of 000s so that the contigs are actually listed in order

[elizabethmcd]

For each assembly rename the contig with this structure:

• Sample name
• Assembler name
• Contig number

For example: comm_1_metaspades_contig000001 so all relevant information is propagated into the assembly contigs

[elizabethmcd]

addressed in #45