macmanes-lab/Oyster_River_Protocol: ORP release 2.2.1

Changelog Version 2.2.0

• FIXED a critical bug whereby the incorrect transcript was picked from a given orthogroup. This fix will potentially improve BUSCO scores dramatically.
• The ORP can now be installed via Docker!! See Dockerfile/Dockerfile
• ADDED a flag to filter lowly expressed transcripts out of the dataset. Implement via TPM_FILT=<float>. The unfiltered assembly is available in the assemblies/working/ folder. We also implement some methods to try and make sure that we don't eliminate any "real" transcripts in this process of TPM filtering.
• ADDED a check to make sure that your read files exist at the specified location.
• FIXED a bug the prevented proper BUSCO checkpointing (thanks @AdamStuckert).
• UPDATED Salmon to 0.13.1 and added the --validateMappings flag to the Salmon commands.
• UPDATED code such that you no longer need to specify main when running oyster.mk.