MultiQC failes with DRAGEN files

[mjlarsen]

Description of bug:
Tried to use the new DRAGEN functionality. But it does not seems to work with the current DRAGEN version: v.3.5.7

MultiQC Error log:

[INFO   ]         multiqc : This is MultiQC v1.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /isilon/drift/drift-genom/dragen-run/09366
Searching 202 files..  [####################################]  100%
[ERROR  ]         multiqc : Oops! The 'dragen' MultiQC module broke...
  Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
  If possible, please include a log file that triggers the error - the last file found was:
    ./09366.germline.vc_metrics.csv
============================================================
Module dragen raised an exception: Traceback (most recent call last):
  File "/root/miniconda3/envs/gatk-germline/lib/python3.7/site-packages/multiqc/multiqc.py", line 569, in run
    output = mod()
  File "/root/miniconda3/envs/gatk-germline/lib/python3.7/site-packages/multiqc/modules/dragen/dragen.py", line 41, in __init__
    samples_found |= self.add_vc_metrics()
  File "/root/miniconda3/envs/gatk-germline/lib/python3.7/site-packages/multiqc/modules/dragen/vc_metrics.py", line 23, in add_vc_metrics
    data = parse_vc_metrics_file(f)
  File "/root/miniconda3/envs/gatk-germline/lib/python3.7/site-packages/multiqc/modules/dragen/vc_metrics.py", line 204, in parse_vc_metrics_file
    data['Insertions'] = data['Insertions (Hom)'] + data['Insertions (Het)']
KeyError: 'Insertions (Hom)'
============================================================
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

[ewels]

Hi @mjlarsen,

Thanks for reporting this. Please could you attach a file that trigger this error? You can zip it if GitHub complains about the file format.

Phil

[ewels]

Maybe @vladsaveliev may know more here?

[vladsavelyev]

Thanks for reporting the issue @mjlarsen, the file and the DRAGEN command used would be really nice to have. I might have missed a use case to test. In any case, I'll add some checks to make sure it won't fail if a metric is absent from a dictionary.

[ewels]

@mjlarsen - Note that the log file says that ./09366.germline.vc_metrics.csv was likely to be the problem here.