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TORCH-Consortium / MAGMA

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
https://doi.org/10.1371/journal.pcbi.1011648
GNU General Public License v3.0
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Implementation of multiqc report generation for the V1 report #221

Open Mxrcon opened 3 months ago

Mxrcon commented 3 months ago

:wave: Hey there, updating what we discussed on #99 regardging the V1 report, I came here to share the first successful run for the V1 accommodating QC report from all samples and a heatmap from the SNP distances.

I'd like to hear your opinion about those changes and how it can be improved for better user experience.

Here s an attachment with the report generated by the pipeline.

The overall changes resume on two steps:

  1. Organize channels for file imporation by multiqc
  2. Add multiqc config file

Kindly, Davi

abhi18av commented 3 months ago

Hi @Mxrcon , I tried to test it locally and it fails with the following message

image
Mxrcon commented 3 months ago

Hi @Mxrcon , I tried to test it locally and it fails with the following message

image

Sorry @abhi18av, rookie mistake i forgot to push the config yaml

abhi18av commented 3 months ago

Thanks for the quickfix @Mxrcon - it is starting to look good.

I have 2 suggestions overall within the scope of multiqc-v1

  1. Allow the multiqc report to be generated even with skip_merge_analysis option enabled for the use-cases where the users might only want to do quick QC on the sequences.

  2. Add a python-script to massage the data being staged into the multiqc process, please look at the comments in the screenshot below

image