peddy module breaks on ts_bcbio sample id

[naumenko-sa]

Hello! Thanks for the great multiqc tool!

Description of bug:
Peddy module of multiqc breaks when running with bcbio

MultiQC Error log:

[INFO   ]         multiqc : This is MultiQC v1.7
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/target_info.yaml'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/contamination/ts_bcbio-verifybamid.failed'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Per_base_N_content.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Per_base_sequence_content.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Per_base_sequence_quality.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Per_sequence_GC_content.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Per_sequence_quality_scores.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Sequence_Duplication_Levels.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/Sequence_Length_Distribution.tsv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/fastqc_data.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/fastqc_report.html'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/fastqc/ts_bcbio.zip'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.background_pca.json'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.het_check.csv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.html'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.ped_check.csv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.ped_check.rel-difference.csv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.peddy.ped'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.sex_check.csv'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/samtools/ts_bcbio-idxstats.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/samtools/ts_bcbio.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/variants/ts_bcbio.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/variants/ts_bcbio_bcftools_stats.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/variants/ts_bcbio_bcftools_stats_germline.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/viral/ts_bcbio-gdc-viral-completeness.txt'
[INFO   ]         multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/ts_bcbio_bcbio.txt'
[INFO   ]           bcbio : Found 1 reports
/bcbio/anaconda/lib/python3.6/site-packages/multiqc_bcbio/bcbio.py:77: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  add_project_info(yaml.load(target_infos[0]['f']))
[INFO   ]        samtools : Found 1 idxstats reports
[ERROR  ]         multiqc : Oops! The 'peddy' 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:
    /home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/peddy/ts_bcbio.sex_check.csv
============================================================
Module peddy raised an exception: Traceback (most recent call last):
  File "/bcbio/anaconda/lib/python3.6/site-packages/multiqc/modules/peddy/peddy.py", line 58, in __init__
    self.peddy_data[s_name].update(parsed_data[s_name])
KeyError: 'ts'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/bcbio/tools/bin/multiqc", line 440, in multiqc
    output = mod()
  File "/bcbio/anaconda/lib/python3.6/site-packages/multiqc/modules/peddy/peddy.py", line 60, in __init__
    self.peddy_data[s_name] = parsed_data[s_name]
KeyError: 'ts'
============================================================
[INFO   ]        bcftools : Found 1 stats reports
[INFO   ]        bcftools : Found 1 stats reports
[INFO   ]          fastqc : Found 1 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : ../../bcbiotx/tmp1n5rgkh7/multiqc_report.html
[INFO   ]         multiqc : Data        : ../../bcbiotx/tmp1n5rgkh7/multiqc_data
[INFO   ]         multiqc : MultiQC complete
' returned non-zero exit status 1.

File that triggers the error:
work/qc/ts_bcbio/peddy/ts_bcbio.het_check.csv

sample_id,depth_outlier,het_count,het_ratio,idr_baf,mean_depth,median_depth,p10,p90,sampled_sites,call_rate,PC1,PC2,PC3,PC4,ancestry-prediction,ancestry-prob
ts_bcbio,False,4,1,0.007679,5982,6078,0.4968,0.5045,4,1,1.234,1.203,5.98,4.946,UNKNOWN,0.3233

work/qc/ts_bcbio/peddy/ts_bcbio.sex_check.csv

error,het_count,het_ratio,hom_alt_count,hom_ref_count,ped_sex,predicted_sex,sample_id
True,6,2,3,0,unknown,female,ts_bcbio

MultiQC run details (please complete the following):

• Command used to run MultiQC: [eg. export PATH=/bcbio/anaconda/bin:"$PATH" && \ export LC_ALL=C.UTF-8 && export LANG=C.UTF-8 && \ /bcbio/tools/bin/multiqc -f -l /home/ubuntu/naumenko/sample_b2/work/qc/multiqc/list_files.txt \ -o /home/ubuntu/naumenko/sample_b2/work/bcbiotx/tmp0bn2vqyo]
• MultiQC Version: [eg. MultiQC v1.7]
• Operating System: [Linux 4.15.0-1048-aws Remove auto-save feature #50-Ubuntu SMP Wed Sep 4 22:03:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux]
• Python Version: [eg. Python 3.6.7]
• Method of MultiQC installation: [bioconda]

Additional context
https://github.com/ewels/MultiQC/blob/master/multiqc/modules/peddy/peddy.py#L60
breaks because previously clean_s_name returns ts instead of ts_bcbio as a sample name.

Sergey

[ewels]

Hi @naumenko-sa,

Thanks for reporting this and apologies for the delay. I think this should now be fixed. If you could test the code in v1.8dev and let me know how you get on with it, that would be great!

Phil