Added components for gatk

[PhilPalmer]

Hey,

I've added bwa, mark_duplicates, base_recalibrator & haplotype_caller components.

Anyone please review, especially @ODiogoSilva

Things I'm not sure on & you might want to check:

• For the parameters in the classes is it best to set default to false rather than null?
• Is there a better solution to ${fasta}.fasta in the templates for base_recalibrator & haplotypecaller?
• I have added mark_duplicates &base_recalibrator to the mapping class. Would it be better if I made a new one eg read_data_manipulation?

[ODiogoSilva]

@PhilPalmer

1 - For non-boolean parameters, the falsy value should be null like you provided. false is mostly reserved for boolean parameters. 2 - There may be, but with additional time. For now we can go with a working solution and later optimize. 3 - Placement is fine.