Simplify software version scrapping

The script https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/devel/bin/scrape_software_versions.py takes for each tool a file containing the version (this file is often the help of the tool) and uses a specific regex to scrap the version. This is quite specific and need to be updated for any new tool used. Since commit 78c72e6d the file containing the version is generated in each module so a cleaner alternative to the script scrape_software_versions.py would be to scrap the tool version directly in each module and return the name of the tool and its version in a channel.