Repurpose GATK module for Sentieon with similar data but changed headers

Ask for help
1

Hey! I want to re-use the gatk/baserecalibrator module for the sentieon qualcal tools. The resulting output seems mostly similar except that the headers are different. They are set here MultiQC/multiqc/modules/gatk/base_recalibrator.py at 9fae75037179f4bece0f1fa96189337e80e8ee2d · MultiQC/MultiQC · GitHub. Is there a way to overwrite them?

I have tried with

sp:
  gatk/base_recalibrator:
    contents: "#:SENTIEON_QCAL_TABLE:Arguments:Recalibration"
    num_lines: 3

but that just finds one of them.

Thank you!

2

Yup, that config is just for the search patterns but that string is used within the parsing of the file in the module code, which is different.

You can see in other Picard submodules that sentieon_algo is often defined to be able to recognise these files. I guess no-one has ever requested this / provided an example file for gatk/base_recalibrator before (also the GATK MultiQC module is a pain to maintain).

Please make a GitHub issue for this and attach an example file :+1: :slight_smile:

Phil

3
1 Like
4

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.