Parse sample ID from BAM

[alkaZeltser]

Update the sample_id param to be parsed from BAM instead of user input.

          1. `patient` isn't being defined, but is set to be used if `params.blcds_registered_dataset == true`.  I'm not sure what that value should be, but it should probably be added to the input and defined on line 8.  

2. Lines 9, 29, 30, 31 can be deleted.
3. I think eventually sample_id should come from the BAM file as shown in the sfitz-update-sample-id-input branch of the template.
4. check_max should be changed to check_limits and imported from pipeline-Nextflow-config; so removed here and changed in base.config
5. set_env should come from pipeline-Nextflow-config
6. setup_docker_cpus should be added from pipeline-Nextflow-config

Originally posted by @sorelfitzgibbon in #27 (comment)