P4 stage2 init options

[dozy]

• allow choice of import formats (BAM/CRAM, FASTQ)
• add optional bambi read2tags processing
• add bwa-mem2 to Dockerfile
• upgrade bambi version in container to 0.18.0
• vtfp 1) extend template preprocessing to subgraph_io sections (in subgraphs); 2) when pruning, only remove ports that do not appear in splice edges (aka replacement edges)
• allow specification of input processing for stage2 analysis
• add static parameter files for stand-alone reanalyses