Update fastqc.py

[y9c]

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated

• There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository or attached to this PR
• Code is tested and works locally (including with --lint flag)
• docs/README.md is updated with link to below
• docs/modulename.md is created
• Everything that can be represented with a plot instead of a table is a plot
• Report sections have a description and help text (with self.add_section)
• There aren't any huge tables with > 6 columns (explain reasoning if so)
• Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
• Module does not do any significant computational work

[ewels]

Better, thanks 👍🏻 Just need to fix black code formatting again and add a changelog entry please.

[ewels]

Bit late now sorry, but this would have been a simpler fix 😉

Suggested change

	except KeyError:
	except (KeyError, ValueError):

[ewels]

Great, thank you!

[ewels]

Hmm, just tested on the example data you provided in #1724 and it does fix the ValueError problem, but I get another new error now:

$ multiqc -f .

  /// MultiQC 🔍 | v1.13.dev0 (f358065)

|           multiqc | Search path : /Users/ewels/GitHub/MultiQC/TestData/data/modules/fastqc/issue_1724
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 1/1
|            fastqc | Found 1 reports
╭───────────────────────────── Oops! The 'fastqc' MultiQC module broke... ──────────────────────────────╮
│ Please copy this log and report it at https://github.com/ewels/MultiQC/issues                         │
│ Please attach a file that triggers the error. The last file found was: ./fastqc_data.txt              │
│                                                                                                       │
│ Traceback (most recent call last):                                                                    │
│   File "/Users/ewels/GitHub/MultiQC/MultiQC/multiqc/multiqc.py", line 654, in run                     │
│     output = mod()                                                                                    │
│   File "/Users/ewels/GitHub/MultiQC/MultiQC/multiqc/modules/fastqc/fastqc.py", line 121, in __init__  │
│     self.read_count_plot()                                                                            │
│   File "/Users/ewels/GitHub/MultiQC/MultiQC/multiqc/modules/fastqc/fastqc.py", line 355, in read_coun │
│     plot=bargraph.plot(pdata, pcats, pconfig),                                                        │
│   File "/Users/ewels/GitHub/MultiQC/MultiQC/multiqc/plots/bargraph.py", line 104, in plot             │
│     if type(cats[0]) is str or type(cats[0]) is unicode:                                              │
│ IndexError: list index out of range                                                                   │
│                                                                                                       │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────╯
|           multiqc | No analysis results found. Cleaning up..
|           multiqc | MultiQC complete

This is why I always insist on having example data - very often it's a game of whack-a-mole with these kinds of errors 😄

[ewels]

Ok, turns out that my suggestion of simply catching the ValueError avoids the secondary crash, so I've just pushed that change to your PR. Hopefully should be good to merge now.

Thanks for reporting and tracking down the bug!