Upgrades to v2

[halexand]

Improvements to codify in the most recent version of eukrhythmic:

• MAD clustering parameters: shift defaults coverage/pid to 0.95/0.95 for MAD clustering
• MAD clustering parameters: add parameters to config.yaml for mmseqs clustering for pid and coverage
• Sample naming in MAD: add project prefix to config.yaml for renaming in MAD
• Abundance filtering: default behavior to run salmon filtering on initial MAD (removal of any contigs with no reads recruited)
• Abundance filtering: add option in config.yaml for user to pass a higher cutoff (e.g. genes with fewer than 10 reads recruiting)
• Software output file: add final output file with version info / environment hashes used in the creation of MAD output. Perhaps add parameters as well? Call it methods-section.txt @shu251 :p
• MAD-info file: add final output info file contianing: number of contigs in MAD (and salmon-filtered MAD), CAGs etc. Add additional info like length distribution and other quast type info?
• Merged annotation table: create final merged annotation table that combines emapper + eukulele outputs
• File clean up: Try to reduce total folder size as much as possible. Maintain CAG final assemblies and some other things but remove intermediate mapping and assembly folders.

Additions to the readthedocs:

• Impact of coverage/pid on MAD: include stats / plot from GO-SHIP and others on impact of clustering parameters MAD
• Discussion of salmon:transdecoder interactions?

[akrinos]

Updates 11 Sept:

• Added percent ID parameter to MAD clustering (5463108)
• Added prefix option to config.yaml (5463108)
• Added merged annotations file (rules/00-clean-up.smk; still beta testing on various projects)

Need to add these changes to the readthedocs.