Refgenie

Added
- added option (`-f`/`--force`) to confirm assets overwriting upfront in `refgenie add` add `refgenie pull`

Changed
- fixed bug in hisat2_index that pointed to the parent folder. The seek key now points to the folder/{genome}, as expected by the tool
- fixed bug in bwa_index that pointed to the parent folder. The seek key now points to the folder/{genome}.fa, as expected by the tool

Changed
- fixed a bug in bowtie2_index recipe that pointed to the parent folder. The seek key now points to the folder/{genome}, as expected by bowtie2
- in `refgenie seek` file existence check is not performed by default

Added
- possibility to execute library module as a script: `python -m refgenie ...`
- support for repeated recipe inputs on CLI (arguments: `--files`, `--assets` and `--params`)
- a possibility to perform file existence check (`-e`/`--check-exists`) in `refgenie seek`

Fixed
- `SyntaxError` in Python 2.7; [155](https://github.com/databio/refgenie/issues/155)

Fixed
- `salmon_partial_sa_index` recipe

Changed
- `refgenie remove` removes the asset relatives links
- `refgenie init` uses `initialize_config_file` method from `refgenconf`
- default input assets for `salmon_sa_index` and `salmon_partial_sa_index` recipes to transcriptomes within the namespace

Added
- `threads` parameter to the following recipes: `dbnsfp`, `salmon_index`, `star_index`

Removed
- documentation regarding `-r`/`--recipe` option in `refgenie build`. It will be removed in the future

Changed
- `refgenie build` command arguments naming scheme: `--{input_name} <path>` to `--files {input_name}=<path>`
- `-r`/`--requirements` in `refgenie build` command to `-q`/`--requirements`
- recipe format: requirements (both assets and inputs) are lists of dicts rather that lists of strings
- `refgenie list` displays current server subscriptions

Added
- `refgenie id` command for asset digest retrieval
- cross-namespace asset relationships support
- `--assets` argument in `refgenie build` command to provide parent assets, if required
- `-r`/`--recipe` in `refgenie build` command argument to provide the recipe for the build
- `subscribe` and `unsubscribe` subcommands to enable server list manipulation in the config file (`genome_servers` entry in the refgenie configuration file)
- new recipes:
- `salmon_sa_index`
- `salmon_partial_sa_index`
- `suffixerator_index`
- `tallymer_index`

Removed
- `-t`/`--tag` in `refgenie build`. Use more flexible `--assets` instead.

Added
- `dbsnp` recipe
- distribute the license file with the package