wfi rewrite v0.4.0

[ammaraziz]

• [x] FIRST Rewrite and restructure snakefile into separate files: common.snk, paired.snk, single.snk, long.snk
• [ ] Update ammaraziz::IRMA to latest version
• [ ] Update rsv irma using the latest data
• [ ] Incorporate nextclade for influenza, rsv, sc2
• [x] Replace cutadapt with fastp
• [x] add pTrimmer for trimming amplicon
• [x] Remove tiled related rules
• [x] Replace R code with python/toyplot specific code
• [x] Add depth masking option
• [ ] #21
• [x] Add csv file as input - use prepare.py