Add flag to check/enforce strandness for a dataset

[emi80]

The pipeline allows to process data with different strandness within the same run. Many time all libraries in a dataset have the same strandness and we would need to (1) check this and stop the pipeline if the automatic strandness inference gives different values or (2) enforce a specific strandness to the process and skip the automatic detection.

The flag could be named --readStrand and have the following values:

• CHECK for (1)
• one of NONE, SENSE, ANTISENSE, MATE1_SENSE, MATE2_SENSE for (2)

[emi80]

For the moment, just adding a --read-strand option to enforce a specific strandness to all processed samples.

By default the option is empty ('') and the pipeline will infer strandness as usual. To enforce a configurations one of NONE, SENSE , ANTISENSE, MATE1_SENSE, MATE2_SENSE must be given.