Whatshap: robust to stdout appended to TSV

[maurya-anand]

HG002_variant_phasing.tsv.zip

──────── Oops! The 'whatshap' MultiQC module broke...────────
Please copy this log and report it at https://github.com/MultiQC/MultiQC/issues
Please attach a file that triggers the error. The last file found was: 04_phaseVars/HG002_variant_phasing.tsv

Traceback (most recent call last):
File "/home/anand/miniforge3/envs/multiqc/lib/python3.11/site-packages/multiqc/multiqc.py", line 712, in run
output = mod()
^^^^^
File "/home/anand/miniforge3/envs/multiqc/lib/python3.11/site-packages/multiqc/modules/whatshap/whatshap.py", line 40, in init
sample, data = self.parse_whatshap_stats(f)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/anand/miniforge3/envs/multiqc/lib/python3.11/site-packages/multiqc/modules/whatshap/whatshap.py", line 109, in parse_whatshap_stats
chromosome = data.pop("chromosome")
^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'chromosome'

[vladsavelyev]

Thank you @maurya-anand for submitting the issue!

I looked into that, and turns out, the MultiQC module didn't expect the "Phasing statistics for sample HG002 from file" section below the table. I wonder if it was appended later to the file. I'm looking into the whatshap code and it looks like it would write the TSV contents to --tsv, and the rest it would write to stdout. So I'm wondering how the two outputs got mixed up. Perhaps --tsv can take stdout as an argument?

Would you be able to give some detail about the version of whatshap, and how exactly it was called to generate the output? That would help us adjust the module properly.

Thank you and sorry about the issue!

[maurya-anand]

Thank you very much, @vladsavelyev for the clarification. I made a mistake by appending the stdout to the same file.

Cheers!

[vladsavelyev]

No problem @maurya-anand! I just made the module robust to this kind of situation, so your issue was helpful anyway.