master yue requests from 12/7 (motif, save files)

[slsevilla]

Describe what enhancement you'd like to see.
Email from Yue

Dear Sam,
 
As I mentioned in our last discussion, macs_narrow method generates XXX_summit.bed and XXX_peaks.xls as output, and macs_broad generates XXX_peaks.xls as output.  They are dropped by current Carlisle pipeline.  I am wondering if we could have an option of keeping it.
 
We discussed with HsienChao, he preferred to use the XXX_summit.bed as input of homer motif analysis and thought it is more accurate. Do you think you can make this modification?  It needs the change of get_peak_file() function in annotations.smk.

To do:

• keep outputs from macs_2 (summig.bed, peaks.xls) (save additional output files from pipeline #104)
• use the summit.bed from either macs2_narrow or macs2_broad as this is the recommend motif file (use summit.bed file as input for homer #105)

[slsevilla]

completed with

• commit 1c8ece0
• commit e2a9a7d