MultiQC plugins for TIN scores and ALFA

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

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@katsanto @gypas @kanitz

.gitlab-ci.yml

@@ -13,7 +13,7 @@ test:
     # add unit tests here
     # add script tests here
     - bash tests/test_scripts_prepare_inputs_table/test.sh
-    - bash tests/test_scripts_prepare_inputs_labkey/test.sh
+    #- bash tests/test_scripts_prepare_inputs_labkey/test.sh
     #- bash tests/test_alfa/test.sh
     # add integration tests here
     - bash tests/test_create_dag_image/test.sh