Have MultiQC output display pipeline summary tables

[jfy133]

Description of feature

ORIGINALLY WE PLANNED TO ADD MULTIQC MODULES, HOWEVER FEW PRODUCES USEFUL SUMMARY STATISTICS. SEE THREAD

Our modules (first release):

• amplify/predict
  • Log file in stdout, however no summary statistcs. Same as output TSV (could summarise number of lines in TSV)
• deeparg
  • No log file, no info in Stdout, output files just tables
• fargene
  • currently no sample-id information in any log file,
  • @louperelo may try updating the tool but little activite on fARGene repo)
• hamronisation
• hmmer/hmmsearch
  • No log files, no stdout info
• macrel
  • There is a log file, slightly odd as it ust spits out a hdeader node and Prodigal output, and hten when there is a hit (I think) it prints the contig name. I guess could count those?
• prokka
• antismash
• ampir
• prodigal

[jfy133]

TODO: Review how many of the tools COULD actually could have MultiQC modules, if only small fraction, drop MultiQC and use use our own custom standardisation scripts.

[jfy133]

Or only make modules for displaying tables from hAMRronisation, the amp-standardisation one from Mortiz and Anan, and something(?) for antisSMASH (that might work as a stadnalone)

[jfy133]

After reviewing all the tools, very few actually produce useful log files or summary statistics (agreed with @louperelo @Darcy220606 @jasmezz ).

We will instead investigate for inserting tables from hAMRonisation, and Anan's and Moritz' tool

[jfy133]

After further thinking, it doesn't make sense to summarise these in MultiQC at all.

Essentially people want a single table of all the tools of the functional category, which then can filter the probability column to find good hits. And nothing more for this step of a workflow.

Therefore, we will drop MultiQC, we will not make the custom shiny app, but rather focus on having a single summary table,and a single 'tool-aggregated' results table per functiaon category.

• ARG: hamronization (we will run twice, one HTML for summary, one for tSV)
• AMP: Moritz's and Anan's python script
• BGC: default output from antiSmash and/or using script from Jasmin