Update Snakefile, README.md, scripts/CheckM.sh, scripts/CheckM2.sh,...

Update Snakefile, README.md, scripts/CheckM.sh, scripts/CheckM2.sh, scripts/CompContPlot.r, scripts/DasTool.sh, scripts/dRep.sh, scripts/Enveomics.sh, scripts/EnveomicsToTable.r, scripts/FilterByQ.sh, scripts/Flye.sh, scripts/GetAbundance.sh, scripts/Gtdbtk.sh, scripts/HifiASM.sh, scripts/MappingForAbundance.sh, scripts/MaxBin2.sh, scripts/MergeCheckMX.r, scripts/MetaBat2.sh, scripts/MiniMap2.sh, scripts/NanoPlot.sh, scripts/SamToBam.sh, scripts/TAD80.r, scripts/TAD80.sh, images/CompContPlot.png, images/4990_A.LengthvsQualityScatterPlot_kde.png, images/4990_B.LengthvsQualityScatterPlot_kde.png, images/4990_C.LengthvsQualityScatterPlot_kde.png, images/4990_D.LengthvsQualityScatterPlot_kde.png, summary.csv, MAGs summary.csv Deleted NanoPlot Results.pdf, images/pipeline.png