Substitute injected .png's for ALFA and TIN scores with our custom MultiQC plugins (repo).
Notable points:
Adjusted MultiQC rule to use our new container.
Removed 2/3 rules on both sides (ALFA, TIN): we do not need any merging, plotting, image concatenation etc. what is left is just the calculation of respective scores.
Pipeline documentation updated accordingly to (1)
Quasi-unit/quasi-integration test for ALFA turned off in the CI. I see that this test was initially calling Snakemake to run 3 ALFA-related rules and generate the final ALFA plots. Since now for ALFA we have only one rule and the main output are per-sample TSV table a "separate 1-rule Snakemake call" is not necessary. Proper unit testing of this functionality should be a bash ALFA call but on a separate input, since everything else (evaluation of wildcards, jobs parallelization) is taken care of in the integration testing.
I will attach here a report after GCN4_project analysis, so that you may take a look at plugins in action:
multiqc_summary.zip
