Error in Picard CrossCheckFingerprints module

[matthdsm]

Error during analysis of CrossCheckFingerprints metrics

$ multiqc --force --zip-data-dir .     
[WARNING]         multiqc : MultiQC Version v1.10.1 now available!
[INFO   ]         multiqc : This is MultiQC v1.10
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /home/projects/sample_tracking/development/NVQ175/MQC
Searching   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 4/4  
[ERROR  ]         multiqc : Oops! The 'picard' 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:
    ./NVQ_Run175-Bravo_prep186.crosscheck_metrics.txt
============================================================
Module picard raised an exception: Traceback (most recent call last):
  File "/software/develop/lib/python3.8/site-packages/multiqc/multiqc.py", line 579, in run
    output = mod()
  File "/software/develop/lib/python3.8/site-packages/multiqc/modules/picard/picard.py", line 65, in __init__
    n["CrosscheckFingerprints"] = CrosscheckFingerprints.parse_reports(self)
  File "/software/develop/lib/python3.8/site-packages/multiqc/modules/picard/CrosscheckFingerprints.py", line 90, in parse_reports
    plot=table.plot(
  File "/software/develop/lib/python3.8/site-packages/multiqc/plots/table.py", line 34, in plot
    dt = table_object.datatable(data, headers, pconfig)
  File "/software/develop/lib/python3.8/site-packages/multiqc/plots/table_object.py", line 196, in __init__
    val = float(samp[k])
TypeError: float() argument must be a string or a number, not 'NoneType'
============================================================

File that triggers the error:
NVQ_Run175-Bravo_prep186.crosscheck_metrics.txt

MultiQC run details (please complete the following):

• Command used to run MultiQC: multiqc --force --zip-data-dir .
• MultiQC Version: v1.10
• Operating System: Ubuntu Server 18.04
• Python Version: Python 3.8.
• Method of MultiQC installation: pip

Additional context
ping @sstadick

Picard command

gatk CrosscheckFingerprints \
--INPUT $EXOME_LIST \
--INPUT $PANEL_LIST \
--OUTPUT $RUN_NAME.crosscheck_metrics.txt \
--CROSSCHECK_BY FILE \
--HAPLOTYPE_MAP $HAPLOTYPE_MAP \
--LOD_THRESHOLD -5.0 \
--REFERENCE_SEQUENCE /Shared/references/reference-production/Hsapiens/hg38/seq/hg38.fa \
--NUM_THREADS 5 --MATRIX_OUTPUT ${RUN_NAME}.crosscheck_matrix.txt

[matthdsm]

I'm going through the code and I think the following
https://github.com/ewels/MultiQC/blob/9c01b0d71a0bdef7ad9f77e93c36ba64c316f228/multiqc/modules/picard/CrosscheckFingerprints.py#L226
Should be INCONCLUSIVE instead of AMBIGUOUS for the formatting to work correctly

[matthdsm]

I think the error comes from the _parse_cli function. The regex tries to extract values using the "old" picard invocation style (using =), the new style uses whitespace
https://github.com/ewels/MultiQC/blob/9c01b0d71a0bdef7ad9f77e93c36ba64c316f228/multiqc/modules/picard/CrosscheckFingerprints.py#L127

[matthdsm]

Confirmed and tested

• by removing the = from the lod_threshold_regex the report is generated.
• formatting is also fixed by using INCONCLUSIVE instead of AMBIGUOUS

so I guess the regex needs to account for a possible = and AMBIGUOUS can be straight out replaced with INCONCLUSIVE. I'm guessing this is an error in the GATK docs.

[matthdsm]

I've opened a PR with the proposed fixes

Cheers
M

[sstadick]

@matthdsm Thanks for tracking that down! Your fixes look correct to me.

[matthdsm]

@ewels I suppose this issue can be closed when/if the proposed PR is merged.

Thanks
M