Split MultiQC output into fastq, library and sample

[marchoeppner]

If we support an input mode in which we support sample IDs and multi-lane sequencing configs, it would make sense to split the MultiQC reports into these three tiers:

the fastq file(s)

• fastqc report

the sequencing library

• MarkDuplicate stats

the sample

• Picard HS
• alignment stats
• picard multiple metrics (CollectMultipleMetrics)