Input samples given only via samplesheet

[fmalmeida]

This solves the following issue:

• diminish pipeline complexity: pass sample always with YAML #35

Now the complexity and amount of pipelines has diminished considerably avoiding possible confusions on how to pass input data. Now, the pipeline only receives the samples data via the samplesheet (--input) and, only the pipeline configurations are available via the config or command line, for example, --skip_kofamscan.

Also, parameters were made simpler:

• --in_yaml is now --input
• --outdir is now --output