Fix custom anchors for kraken

[jchorl]

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated
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This change broke custom anchors for the kraken module: https://github.com/ewels/MultiQC/pull/1372/files#diff-10bfc7513ddf0bd9fd13bbb456bb610f9d45592b3a2e9337bc44a6dba05c335eR29

I don't believe find_log_files should use the anchor (which is an html detail as best I understand).

I'm not uber confident on this fix, but it does revert to how it was before, and fix our issues.

Without fix:

root@58ce75507ca9:/src/MultiQC_TestData/data/modules/kraken# multiqc -f .

  /// MultiQC 🔍 | v1.18.dev0

|           multiqc | Search path : /src/MultiQC_TestData/data/modules/kraken
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 16/16  
╭───────────────────────────────── Oops! The 'kraken' 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: ./v2.0.8_beta/sample1.kraken2.report  │
│                                                                                                              │
│ Traceback (most recent call last):                                                                           │
│   File "/usr/local/lib/python3.12/site-packages/multiqc/multiqc.py", line 691, in run                        │
│     output = mod()                                                                                           │
│              ^^^^^                                                                                           │
│   File "/usr/local/lib/python3.12/site-packages/multiqc/modules/kraken/kraken.py", line 51, in __init__      │
│     for f in self.find_log_files(self.anchor, filehandles=True):                                             │
│   File "/usr/local/lib/python3.12/site-packages/multiqc/modules/base_module.py", line 139, in find_log_files │
│     for f in report.files[sp_key]:                                                                           │
│              ~~~~~~~~~~~~^^^^^^^^                                                                            │
│ KeyError: 'not_kraken'                                                                                       │
│                                                                                                              │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
|           multiqc | No analysis results found. Cleaning up..
|           multiqc | MultiQC complete

With fix:

root@58ce75507ca9:/src/MultiQC_TestData/data/modules/kraken# multiqc -f .

  /// MultiQC 🔍 | v1.18.dev0

|           multiqc | Search path : /src/MultiQC_TestData/data/modules/kraken
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 16/16  
|            kraken | Found 12 reports
|            kraken | Kraken2 reports of different versions were found
|           multiqc | Report      : multiqc_report.html   (overwritten)
|           multiqc | Data        : multiqc_data   (overwritten)
|           multiqc | MultiQC complete

Here is a TestData report with the fix (zipped so github allows it):

multiqc_report.zip

Here's how I tested:

1. Add a config yaml in MultiQC_TestData/data/modules/kraken/multiqc_config.yaml:

   module_order:
     - kraken:
         anchor: not_kraken

2. Installed multiqc locally

3. cd to the kraken testdata dir and run

cc @vladsavelyev

[vladsavelyev]

Thank you @jchorl for the pull request, and sorry about the issue!

The reason it used self.anchor there instead of a hardcoded "kraken" is that this module is also reused by bracken which would override that tag in order to reuse the code.

You are correct that it shouldn't be self.anchor though. I forgot that it can be overridden in config which would break things. Just fixed it by passing another variable sp_key to the module constructor.

Thanks again!

[jchorl]

Thanks!