Multiqc customised plugins

Create customised graphs in MultiQC for:

• Alfa
• TIN scores

Probably addition of PCA within this report

Krish has forked the MultiQC repo into his GitHub and created two branches to work on Alfa and TIN score plots.

TIN score (he named the module zarp):
https://github.com/krish8484/TIN_Scores/tree/master/multiqc/modules/zarp

Alfa:
https://github.com/krish8484/MultiQC/blob/master/multiqc/modules/alfa

changed milestone to %downstream

Remaining: Ask people of official repo to incorporate our instances. Otherwise fork will need maintenance.

We decided that:

• For the TIN score we will write an official MultiQC module (if our TIN format matches the original TIN -> I have to check that)
• For ALFA we will write our own plugin so that later MultiQC can be built together with it from the source (https://github.com/zavolanlab/multiqc-plugins); maybe later we will turn it into an official module as well.

I have looked closer into the i/o formats for the official tin score calculating program (part of rseqc package) and our custom repo based on that program.

As for the Command Line arguments, the two scripts are consistent, check the official docs:

• http://rseqc.sourceforge.net/#tin-py
• https://git.scicore.unibas.ch/zavolan_group/tools/tin_score_calculation

With the small difference that out in-house script takes additionally --names=SAMPLE_NAMES.

However, the output tables differ.
For our script we have:

transcript	sample_1
ENST00000303113	10.0
ENST00000427445	20.0
ENST00000430792	30.0

For the original program there is:

geneID  chrom   tx_start        tx_end  TIN
ABCC2   chr10   101542354       101611949       67.6446525761
IPMK    chr10   59951277        60027694        86.383618429
RUFY2   chr10   70100863        70167051        43.8967503948

If we were to write an official module for parsing the original tin.py program we would have to overcome that differences. Therefore, for now, me and Krish will develop a MultiQC plugin, just as for ALFA (as we already have an idea of how to do proceed).

Our repository with MultiQC plugins of the Zavolab:
https://github.com/zavolanlab/multiqc-plugins

added Doing label

mentioned in issue #109 (closed)

marked the checklist item Alfa as completed

marked the checklist item TIN scores as completed

mentioned in commit fab75506

Fixed in !79 (merged)

closed