Dragen module broken in latest version

The dragen plugin seems to be broken in the latest version (1.22.2). It is probably related to the update in the plotting backend.

The error message:

dragen/dragen_gc_metrics.py: Invalid LinePlot plot configuration
unrecognized field 'namespace'

Conflicting lines are dragen_gc_metrics.py:60 and dragen_gc_metrics.py:76. It seems to be something easy to fix so I’m willing to make a PR though I wonder which field should be used instead of ‘namespace’.

José, sorry about the issue, we just fixed it with DRAGEN: fix gc_metrics submodule by vladsavelyev · Pull Request #2629 · MultiQC/MultiQC · GitHub.

Turns out we didn’t have test coverage for this part of dragen, so didn’t catch this bug with our tests. I wonder if you could share the *.gc_metrics.csv file by any chance so we can put it into test-data/data/modules/dragen at main · MultiQC/test-data · GitHub?

Thanks for the quick fix! I cannot share the data but I can tell you how the file looks so you can easily generate a file with simulated data.

GC BIAS DETAILS,,Windows at GC [0-100],<number of windows>,<fraction of all windows>
GC BIAS DETAILS,,Normalized coverage at GC [0-100],<average coverage of all windows at given GC divided by average coverage of whole genome>
GC METRICS SUMMARY,,Window size,<window size in base, typically 100>
GC METRICS SUMMARY,,Number of valid windows,<total number of windows used in calculations>
GC METRICS SUMMARY,,Number of discarded windows,<total number windows discarded due to more than 4 masked bases>
GC METRICS SUMMARY,,Average reference GC,<average GC content over all valid windows>
GC METRICS SUMMARY,,Mean global coverage,<average genome coverage over all valid windows>
GC METRICS SUMMARY,,Normalized coverage at GCs <GC range>,<average coverage of all windows at given GC range divided by average coverage of whole genome>
GC METRICS SUMMARY,,AT Dropout,<Calculated AT dropout value>
GC METRICS SUMMARY,,GC Dropout,<Calculated GC dropout value>

An example with made up numbers:

GC BIAS DETAILS,,Windows at GC 0,153008,0.05
GC BIAS DETAILS,,Windows at GC 10,226522,0.08
GC BIAS DETAILS,,Windows at GC 20,13965431,0.5
GC BIAS DETAILS,,Windows at GC 50,77304405,3.02
GC BIAS DETAILS,,Windows at GC 75,2197298,0.5
GC BIAS DETAILS,,Windows at GC 100,639,0.000
GC BIAS DETAILS,,Normalized coverage at GC 0,0.1
GC BIAS DETAILS,,Normalized coverage at GC 10,0.5
GC BIAS DETAILS,,Normalized coverage at GC 20,0.9
GC BIAS DETAILS,,Normalized coverage at GC 50,1.2
GC BIAS DETAILS,,Normalized coverage at GC 75,1.2
GC BIAS DETAILS,,Normalized coverage at GC 100,0.01
GC METRICS SUMMARY,,Window size,100
GC METRICS SUMMARY,,Number of valid windows,3000000
GC METRICS SUMMARY,,Number of discarded windows,1000000
GC METRICS SUMMARY,,Average reference GC,50.5
GC METRICS SUMMARY,,Mean global coverage,9
GC METRICS SUMMARY,,Normalized coverage at GCs 0-19,0.5
GC METRICS SUMMARY,,Normalized coverage at GCs 20-39,1.0
GC METRICS SUMMARY,,Normalized coverage at GCs 40-59,1.1
GC METRICS SUMMARY,,Normalized coverage at GCs 60-79,1.3
GC METRICS SUMMARY,,Normalized coverage at GCs 80-100,0.7
GC METRICS SUMMARY,,AT Dropout,4.5
GC METRICS SUMMARY,,GC Dropout,0.5

if you create a file XXX.gc_metrics.csv with this content it should hopefully be enough to add it as a test data for this part of the module.

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By the way, do you have any idea when this fix will be released?

We’re aiming for a release at around the end of the week…

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Hi Phil! Nice :slight_smile:

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