Merge DEV

This PR has:

• CWL code, moved to an dev version in order to use conditionals.
• Changes for https://github.com/EBI-Metagenomics/emg-viral-pipeline/issues/13
• Changes for https://github.com/EBI-Metagenomics/emg-viral-pipeline/issues/12
• Fix for lenght filtering script, memory problem reported by Alex A.
• Mashmap optional step in CWL and Nextflow
• Travis build for CWL and python scripts. Not sure how to write tests for Nextflow, at least a validation of the code (I'll dig into this).

I've tested this locally and it's working, I'll move the code to the cluster to run some tests.