Trimmomatic logs not parsed properly

[cgirardot]

Description of bug:
I try to assemble a report with Trimmomatic logs (amongst others). Trimmomatic was run in Galaxy, all the logs therefore refer to a fastq_r1 input file used to name the sample. To circumvent this, I am using the instruction:

extra_fn_clean_exts:
    - type: regex_keep
      pattern: '[0-9]+_mATAC_t[0-9]{1,2}'

to extract sample names from file names like 180518_mATAC_t1_1_trimmomatic.err.

Strangely this instruction is ignored for trimmomatic logs while the regex perfectly works for other modules ; so I end up with a single sample (i.e. fastq_r1) in the report section.

MultiQC Error log:

[INFO   ]         multiqc : This is MultiQC v1.6
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching 'qc/trimmomatic/'
[INFO   ]     trimmomatic : Found 1 logs
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : trimmo_test.html
[INFO   ]         multiqc : Data        : trimmo_test_data
[INFO   ]         multiqc : MultiQC complete

File that triggers the error:
Attached is a zip with 10 logs and the config file

trimmomatic.zip

MultiQC run details (please complete the following):

• Command used to run MultiQC:
  multiqc -c multiqc_ATAC_config.yaml -n trimmo_test qc/trimmomatic/

• MultiQC Version: MultiQC v1.6

• Operating System: CentOS Linux release 7.4.1708 (Core)

• Python Version: Python 2.7.15

• Method of MultiQC installation: conda

[ewels]

Thanks for the detailed issue 👍 I'll look into it as soon as I can.

Phil

[ewels]

Hi @cgirardot,

The problem here is that Trimmomatic gets it's sample names from the command line used. As you pointed out, this is the same for every file in your case. The extra_fn_clean_exts only works with the sample name that has been collected, so doesn't help in this case as the filename is not used at all.

To get around this, I've added a new option to the code which allows you to set a config flag to tell the module to use the filename instead of the file contents. To use it, add the following config option:

trimmomatic:
    s_name_filenames: true

Once you have this, everything should work as excepted.

Let me know how you get on!

Phil

[cgirardot]

right on time fro Christmas !

Thx

[cgirardot]

this is working great , thanks again.

[ewels]

Hi all,

Old issue, but wanted to note that I have added this behaviour as a general feature for any module / file search pattern in fa84c47 and will be included in the MultiQC v1.11 release.

The documentation for this new feature is here: https://multiqc.info/docs/#using-log-filenames-as-sample-names

I haven't removed the Trimmomatic-specific config described above, so that should still work. But I would recommend switching to the new system if you can as it may be removed in the future.

Cheers,

Phil