With convert_gtc2bcf, contamination and intensity checks should be done using BCF.

[rajwanir]

With convert_gtc2bcf switch added in PR #346, the intensity and contamination sub_workflows should use the bcf file instead of GTC/IDAT. These sub_workflow should execute essentially as in BCF entry_point created in PR #314

Tasks

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1. Create a rule to symlink bcf: This will symlink cfg.config.user_files.bcf to "sample_level/samples.bcf" so both BCF entry_point and convert_gtc2bcf can reference the same file.
2. Add convert_gtc2bcf as an additional condition in contamination and intensity subworkflow where bcf file should be used instead.