Add parameters for percent contamination threshold/depth coverage/percent read length trimming for green and orange status

Write the metagenomic fasta file directly in the variantcall/ folder, as ${PREFIX}.consensus.fasta + Create a full report.json file with NA values for metagenomics input

Added -redo to IQTREE2 to ensure that the tree is always rebuilt, even if a tree with the same strains already exists.