standard report trimming tools

[Alejandra Cervera]

it would be nice to have Trimmomatic, Fastx, and TrimGalore all output a file called summary (or whatever) that has the following columns:

• Input_Reads
• Output_Reads
• Discarded (which can be a percentage or not)
• Forward_Only_Surviving_Percentage (only for paired end)
• Reverse_Only_Surviving_Percentage (only for paired end)

I have already done Trimmomatic, please look at the stats file there and follow the example.

I have also done TrimGalore, so only FastX missing.

The last two columns can always be calculated from the first two but it is good to have that info since it will be used in QCFasta.

[Alejandra Cervera]

fixed