refrain from *txt suffixes
in https://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/blob/devel/mflow/workflows/life-science/StructureBasedScreening/Snakefile refrain from txt suffixes
Reasoning: txt is an arbitrary designator, which mostly indicates human readable text. pdbqt is a text file, albeit non-prosa.
To distinguish in- from output us underscore separated semantics. E.g.
rule prepareDocking: input: path.join(PREPARED_DIR, "receptor", "{receptorID}.pdbqt") output: path.join(OUTPUT_DIR,"receptor","{receptorID}.txt")
would become
rule prepareDocking: input: path.join(PREPARED_DIR, "receptor", "{receptorID}.pdbqt") output: path.join(OUTPUT_DIR,"receptor","{receptorID}_prep.pdbqt")
where 'prep' is merely a suggestion.