Rules should not explicitly refer to scripts as inputs

[rdmorin]

The setting of scripts used by specific rules as explicit inputs to that rule is problematic. When a second user is using a different copy of the lcr-modules repo the pipeline will then force re-running of the rules that depend on that input file. For example, if the following rule is run by user B (let's call her Laura... no, Dr. H) on a partially completed run of the pipeline (run by user A, or Dr. M), it will trigger a complete rerun of the pipeline by user A. I see no reason a script should ever be an input to a rule. These should be changed to params or, possibly better yet, just put into "src" and used by exporting that directory to the PATH at the start of the rule.

rule _manta_augment_vcf:
    input:
        variants_dir = str(rules._manta_run.output.variants_dir),
        aug_vcf = CFG["inputs"]["augment_manta_vcf"]