Opened 9 years ago
Closed 9 years ago
#743 closed defect (fixed)
The second trimmomatic step in demux script may not include options
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | trivial | Milestone: | Reggie v3.2 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
When generating the script for the second trimmomatic step the options specified may not be included since there is an incorrect check:
if (demux_trimmomaticOptions1 != null)
{
trimCmd2 += " " + demux_trimmomaticOptions2;
}
The if statement should check demux_trimmomaticOptions2. Fortunately both options are required and should never be null at this stage.
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(In [3141]) Fixes #743: The second trimmomatic step in demux script may not include options