SciLifeLab/bcbb — pull request #195 by vals (2012-08-20 09:59:59+00:00)
Title: Feature/save diskspace dedupping

Here is a copy of the information in the Trello card:

The `picard_mark_duplicates` operation in the pipeline is only run as either part of the recalibration process (`recalibrate_sample`) (which we don't do) or as part of the metrics-generation process (which we do). If it's run in the last case, it doesn't take the "`save_diskspace`" option into account.
Modify the code to run the dedupping step after the merging of bam files and observing the `save_diskspace` step.

https://trello.com/card/dedupping-in-pipeline/4f85364e8c672a1d5b4cf2bc/91

In a few words: I added a call to `save_diskspace` in the metrics generation if it creates a dup_bam which is only used inside `_get_current_dup_metrics()`.

The code needs review and then possibly merge, by one of @b97pla , @brainstorm or @percyfal