Fixed peddy validation, sample id cleanup for underscore stripping, simplified sample preparation processes

• Fixed and simplified peddy validation script after moving to bin folder
• Sample ids were having underscores stripped when config YAML generated, this is now fixed (awkwardly)
• Sample preparation process simplified, we do not need to run bcbio_prepare_samples.py when we have already merged reads explicitly in the previous process

requested review from @mwham

assigned to @ameyner2

added 10 commits

• 4db33f0a...eddf83bc - 9 commits from branch master
• b4c1f558 - Merge branch 'master' into 'peddy-validation-to-bin'

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added 1 commit

• fff9313f - Fixed tests to reflect changes in peddy validation script and removal of bcbio_prepare_samples.py

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approved this merge request

merged

mentioned in commit 1b7664b0