Refchef

Fix
* fix logging (e8cad2d9532cbc3d316f741e0d7547199a54dbe3)
* fix logs in refchef cook (66d1aafb16c4dfc3199c9d5ed5610e4a7a6da290)
* fix species column in refchef-serve flask app (9b32cc54da5089d602e14859e809bd0bc5fc6377)

Documentation
* cleaning up the documentation (dd0b1beb9ea37ef4a67b6eaa961c8999b3fc289a)
* separated the docs into distinct pages, added some use case figures (which need to be fixed still) (2939e300c8c57c8d71e239fdbd4792e1c1a3f7f7)
* added some more details to installation.md, added some figures to index.md, changed specs.md to be more about all file specs and added links betw usage and specs files (84ba24731fede0c2b023f93c1bb5cd72bd21f834)
* adding some more details on installation, updated quickstart.md and index.md to (fb7cf068283127e5b74b673bcdf4f1f6d1842a8c)

Feature
* add ability to select metadata based on reference name to refchef-menu (45ed681025c6e3b661d0e59949f0483d69974cd4)

Fix
* fix date issue with yaml merge (fd5aacbe1a87d6a199de31a2a128fb71acfefab4)
* fix yaml merge issue (c4ea5fb6469de48999575545c2b071ade67e136d)
* we are adding an append argument so that master.yaml can be appended without executing commands (85f66d4674e8e4351657239fe65ac0add7f957f3)
* remove print statement from metadata (b96970b6740a183746f0bf34b1acec8fabf5774a)
* fix metadata table build (cfe9f71652f7e17aead6fb594a98857880532554)

Breaking
* s (u)

Documentation
* added details about yaml specs, config specs, and file outputs (594691f2472ca2003cbe1a6849dff4d8d75acbbc)
* adding more details on usage of cook and menu, also expanding on the master.yaml file (2f9a60e15f13724a77b86a8242dc516957ba4f0a)
* adding new examples of adding multiple index files (3d29bb9808112988b91dfb10b60231d162d96e37)
* fixing some merge conflicts (7fb02d2a9d65f60a7cf3363ec28b4d02848e52cc)
* reformatting usage.md (b4887561ffa9047f09a64c78448f470348c8b309)
* updated master.yaml metadata specs, attempted to add some more details about adding a bwa reference (not sure if this is right), still need to add documentation on use case where index is already present somewhere else and it is added to the master.yaml (5561af96959fe621f8cef93d7dba8c08a7b980b6)
* fixing some formatting (6a2d73c7dace42508c3cf21a02902335115143bc)
* fixing links to other subsections of usage.md (886a86fedc2da74bed40daa3860f6253e1807c0e)
* continuing to reorganize -- added some more introductory information about refchef (0bfa8761696f99ca2e75ae0d799b1e27e4bf48ef)
* added to description field in modified master.yaml file (see issue 29) (ecfdc661c35e3f6caef31dd27163aa944a15ce46)
* regarding issue 29, adding more metadata (7beeb93860306157b3515e5beba55ae4f6f1b4b4)

Fix
* fix cfg docs (135b6d11bb87443a327bc33e919579d30ae6e320)
* add uuid1 in case there's no checksum file (46a8d5d683d6443cb06655bb9169781b4a6c883c)
* fix logging (608e3fdb2299487265bc8faa6063917635a1c5a0)

Documentation
* added more details and examples of usage (bee860af1933a05c14b3c43cbfc0d24b8daf36c8)
* add yaml specs (68c0e79bc339d7bd87b78287456771c58595a98c)

Fix
* remove verbose from refchef-cook menu (ec925148fe863d415a87bcfd21a23898be4de778)

Documentation
* add contributing section to docs (copy from readme) (c591a10d356c2332e54bb713311dda800f15f283)

Fix
* try to force a patch version (02aab848a67fe19885a98a374a393741e067a928)

Fix
* set pytest to 3.6, breaking tests (ceea798c2c1a065487a1eb77317d809aea43f8d0)