Add an option to run the older bwa-mem instead of bwa-mem2

[Nicklas Nordborg]

There are some issues with bwa-mem2 that causes it to crash. It is some kind of memory-related error and the error message may differ from time to time. Typical are: double free or corruption, Segmentation fault and invalid pointer.

The original bwa-mem (version 0.7.17) has been tested on one of the problematic samples and it seems to be working.

[Nicklas Nordborg]

R1 and R2 with 250 read pairs that causes bwa-mem2 to fail

[Nicklas Nordborg]

In 7178:

References #1486: Add an option to run the older bwa-mem instead of bwa-mem2

A new version of the container that include both bwa 0.7.17 and bwa-mem2 2.2.1

[Nicklas Nordborg]

In 7179:

References #1486: Add an option to run the older bwa-mem instead of bwa-mem2

Added a configuration "parameter-set" that uses the original "bwa" aligner instead of "bwa-mem2". There are some minor changes in the script to make sure that "bwa-mem2" is selected by default and that log/progress messages uses the actual program name in the output.

[Nicklas Nordborg]

In 7180:

References #1486: Add an option to run the older bwa-mem instead of bwa-mem2

Updated the configuration with the new values for the number of cores to use for various analysis steps. Using 32 cores for bwa-mem2 turned out to be inconvenient since the computation nodes have 64 cores. By changing to 24 cores there is still room for a 16-core job or 2 8-core jobs to execute alongside the alignment on each node.