[SUGGESTION] Migrating config from params.sc.<tool>.* to params.tools.<tool>.*

[dweemx]

Is your feature request related to a problem? Please describe.
Not related to a problem.
The goal is to unify and to improve the config structure by moving from params.sc.<tool>.* to params.tools.<tool>.*.
Important:

• This new config schema should be backward compatible!
• This will be a breaking change: the old configs will likely not work anymore
• Several params entries have moved to the params.utils scope: scope, cell_annotate, cell_filter, file_converter, file_concatenator, file_cleaner, sample_annotate, star_concatenator

Tools:

• celda
• cellranger
• directs
• dropletutils
• dropseqtools
• fastp
• flybaser
• harmony
• pcacv
• picard
• popscle (previously done)
• pycistopic (previously done)
• scanpy
• scenic
• scrublet
• singlecelltoolkit (previously done)
• sinto (previously done)
• soupx
• sratoolkit
• star
• trimgalore (previously done)
• utils

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