Issue with parsing fastp json file

[danfulop]

Description of bug

I got this error regarding fastp's JSON file:

File that triggers the error

5fastp.json.zip

MultiQC Error log

/// MultiQC 🔍 | v1.12

  |           multiqc | Search path : /home/ubuntu/git.repos/pipeline-bacteria-rnaseq/work/8e/cd577ca94335fa95c4214d9b2d4307
  |             rseqc | Found 3 read_distribution reports
  |             rseqc | Found 3 gene_body_coverage reports
  |             rseqc | Found 3 inner_distance reports
  |             rseqc | Found 3 read_gc reports
  |             rseqc | Found 3 read_duplication reports
  |             rseqc | Found 3 infer_experiment reports
  |             rseqc | Found 3 bam_stat reports
  |            salmon | Found 3 fragment length distributions
  |              star | Found 6 reports
  ╭────────────────────────────────────────────────────── Oops! The 'fastp' 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: ./fastp/5fastp.json                                                             │
  │                                                                                                                                                        │
  │ Traceback (most recent call last):                                                                                                                     │
  │   File "/home/ubuntu/miniconda3/envs/pipeline-salmon-rna-seq/lib/python3.9/site-packages/multiqc/multiqc.py", line 651, in run                         │
  │     output = mod()                                                                                                                                     │
  │   File "/home/ubuntu/miniconda3/envs/pipeline-salmon-rna-seq/lib/python3.9/site-packages/multiqc/modules/fastp/fastp.py", line 48, in __init__         │
  │     self.parse_fastp_log(f)                                                                                                                            │
  │   File "/home/ubuntu/miniconda3/envs/pipeline-salmon-rna-seq/lib/python3.9/site-packages/multiqc/modules/fastp/fastp.py", line 162, in parse_fastp_log │
  │     cmd = parsed_json["command"].split()                                                                                                               │
  │ TypeError: 'int' object is not subscriptable                                                                                                           │
  │                                                                                                                                                        │
  ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
  |           multiqc | Compressing plot data
  |           multiqc | Report      : multiqc_report.html
  |           multiqc | Data        : multiqc_data
  |           multiqc | MultiQC complete

[ewels]

Thanks @danfulop!

The reason that MultiQC wasn't working is because your JSON file is not what MultiQC (or, I guess, you) is expecting:

30596

This is technically valid JSON, so the existing check that the JSON file can be parsed went through ok. However, as soon as the code tried to load anything in the file it crashed.

I've updated MultiQC to check that at least one expected key is present. Now instead of a hard crash you get an error message that the log file could not be parsed.

Thanks!