picard hs_metrics: Handle null (0 int) values

[tomSimonet]

Hello,

just a really minor issue: the picard module broke, analysing hs_metrics, when one metric file was produced from a failed sequencing, with a lot of null values;
I think the probkem may come from a ? value in the FOLD_80_BASE_PENALTY field, which could not be computed in this case

with the hs_metrics file from the failed sequencing :

$ python3 -m multiqc -o Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23 Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23/
[INFO   ]         multiqc : This is MultiQC v1.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /home/thomas/Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23
Searching 5 files..  [####################################]  100%          
[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:
    Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23/Z338_umiFlt_hs_metric.txt
============================================================
Module picard raised an exception: Traceback (most recent call last):
  File "/home/thomas/progr/Anaconda/lib/python3.6/site-packages/multiqc/multiqc.py", line 569, in run
    output = mod()
  File "/home/thomas/progr/Anaconda/lib/python3.6/site-packages/multiqc/modules/picard/picard.py", line 65, in __init__
    n['HsMetrics'] = HsMetrics.parse_reports(self)
  File "/home/thomas/progr/Anaconda/lib/python3.6/site-packages/multiqc/modules/picard/HsMetrics.py", line 182, in parse_reports
    plot = table.plot(data, _get_table_headers(data))
  File "/home/thomas/progr/Anaconda/lib/python3.6/site-packages/multiqc/plots/table.py", line 49, in plot
    return make_table ( dt )
  File "/home/thomas/progr/Anaconda/lib/python3.6/site-packages/multiqc/plots/table.py", line 139, in make_table
    val = header['modify'](val)
  File "/home/thomas/progr/Anaconda/lib/python3.6/site-packages/multiqc/modules/picard/HsMetrics.py", line 279, in <lambda>
    headers[h]['modify'] = lambda x: x * config.base_count_multiplier
TypeError: can't multiply sequence by non-int of type 'float'
============================================================
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete`

after removing this null-values containing hs_metrics file from the directory:

$ python3 -m multiqc -o Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23 Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23/
[INFO   ]         multiqc : This is MultiQC v1.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /home/thomas/Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23
Searching 4 files..  [####################################]  100%          
[INFO   ]          picard : Found 4 HsMetrics reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23/multiqc_report.html
[INFO   ]         multiqc : Data        : Bureau/MBarito/Qiaseq-Multimodal/DNA/umi_Flt_bam/hs_metrics_v2.23/multiqc_data
[INFO   ]         multiqc : MultiQC complete`

Example outputs:

E10981_umiFlt_hs_metric.txt
E11642_umiFlt_hs_metric.txt

[ewels]

Thanks for reporting this and supplying example data @tomSimonet - should be simple enough to fix 👍🏻

[ewels]

Fixed in #1471 by @ErikDanielsson, will be including in the upcoming v1.11 release.

Thanks for reporting @tomSimonet - shout if any part of it doesn't work how you expect :)