remove _workflow_result

code-deduplication: mburnett, gsanders
remove lsf_queue

code-deduplication: mburnett, gsanders
move _promote_staged_data to base

code-deduplication: mburnett, gsanders
extract versions

code-deduplication: mburnett, gsanders
move has_version to base

code-deduplication: mburnett, gsanders
whitespace

code-deduplication: mburnett, gsanders
move _create_temp_directories to base

code-deduplication: mburnett, gsanders
extract _ensure_chromosome_list_set

code-deduplication: mburnett, gsanders
extract _ensure_chromosome_list_set

code-deduplication: mburnett, gsanders
remove unused variables

code-deduplication: mburnett, gsanders
remove unused variables

code-deduplication: mburnett, gsanders
extract add_bams_to_input

code-deduplication: mburnett, gsanders
extract set_output

code-deduplication: mburnett, gsanders
whitespace

code-deduplication: mburnett, gsanders
remove useless comment

code-deduplication: mburnett, gsanders
rename reference on input_connector

code-deduplication: mburnett, gsanders
extract get_reference

code-deduplication: mburnett, gsanders
extract workflow_xml

code-deduplication: mburnett, gsanders
refactor _detect_variants in MethRatio

code-deduplication: mburnett, gsanders
move _detect_variants to base

code-deduplication: mburnett, gsanders