Running a mask/align job as debug for a non-debug demux doesn't change the outcome

[Nicklas Nordborg]

The help text for the debug option says:

When running in debug mode only part of the sequenced data is used and temporary files are not removed from the cluster node.

While the last part is true, the first part is not, since it assumes that the demuxed data has been created with debug as well.

[Nicklas Nordborg]

I think there are two things that should be fixed:

• Add -u parameter to bowtie in the first step. This should automatically limit the input to tophat.

• Add 'debug' suffix to the data files directory so that debug runs are not mixed up with real runs.

[Nicklas Nordborg]

(In [2848]) Fixes #675: Running a mask/align job as debug for a non-debug demux doesn't change the outcome

[Nicklas Nordborg]

(In [2849]) References #675: Running a mask/align job as debug for a non-debug demux doesn't change the outcome