Add alignment QC steps that can be added into the final multiQC report

[nrminor]

Right now, we only report FASTQ read statistics for primer-trimmed amplicon reads. Still, users are typically interested both in the quality of the data that goes into alignment, as well as the alignment itself. As part of building out our quality control subworkflow, we should introduce samtools flagstat, which is supported by multiQC, and maybe also cramino.