feat: set intermediate and final output files

[deliaBlue]

Fixes #86

• add a directory to store the intermediate files in config_template.yaml and config_schema.json
• add the intermediate files path in all the snakemake files
• add the onfailure and onsuccess handlers in the main Snakefile so intermediate files are not lost if the workflow fails and removed otherwise.
• redirect the intermediate files to the new directory in the sub-workflows
• add the section "Expected output files" in the main README.md with a brief explanation of the files that are kept by default and how to keep the intermediate ones
• update the finish rules in pipeline_documentaion.md
• update the rule graph
• add the CLI option --no-hooks to all the tests in order to keep checking all the files in the CI tests
• update the expected output to match the new location of the intermediate files

[uniqueg]

Good work :) Couple of comments, but shouldn't be all that much

[uniqueg]

I'll approve this now. You can see how/whether you address (or not) the two open conversations and then merge.