Refactor CI/CD testing: eliminate redundancy
There is some redundancy in the current testing as there are multilane and not multilane separate samples tables and config file. it is better if we can merge some of these tests to avoid code redundancy
Context
A diff on the original and multi-lane integration test files (each 90 lines!) yields:
30c30
< --configfile="../input_files/config.mutliple_lanes.yml" \
---
> --configfile="../input_files/config.yaml" \
41c41
< --configfile="../input_files/config.mutliple_lanes.yml" \
---
> --configfile="../input_files/config.yaml" \
so only 2 lines are different, just a different config file in two places. This can be easily parameterized by passing a CLI argument. Pretty much the same goes for local vs Slurm execution tests (in those same integration tet folders), where there are also only a few lines difference (could be changed with a command-line flag).
Having lots of repeated code is a maintenance hell because of copy/paste errors (see below) and divergent code evolution.
Suggestion
Have a single test script for all 4 current integration tests, with e.g., this example usage:
test.sh --config="config.yaml" --env="slurm"
Also check other test scripts for similar redundancy.