Implement alignment for the DNA WGS pipeline
See #1464 for background.
The first alignment step is done separately for each sample.
bwa-mem2 should be used for alignment from FASTQ files. After the alignment several
samtools steps are used for sorting/merging, etc. The end result should be a single BAM file with aligned and unaligned sequences. We will probably produce some statistics also and some values will be imported as annotations into BASE.