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.
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