Troubleshooting of the pipeline

[leilaicruz]

In the branch pipeline_test you can find a short file of instructions for first use of the pipeline in a new linux computer.
This is a file I did after testing the pipeline in my linux laptop, where I had to face some small issues mainly regarding software installations and computer paths.

• There is also a pipeline bash script for first use that the only change is that you need to index the reference genome before the alignment , but that is only necessary in the first use. I recommend to run this one for the 1st use.