Hey! Is there a way to add in more columns for a t...
# multiqcr
Rike Hanssen
09/02/2024, 8:54 AMHey! Is there a way to add in more columns for a tool into the general stats table, that are not parsed in the modules script? For example: https://github.com/MultiQC/MultiQC/blob/35555b12abf83ef1f2f44f03745243c3b16512e6/multiqc/modules/fastp/fastp.py#L339 I want to also get number of reads before filtering which should be available in the
jsonp
Phil Ewels
09/02/2024, 8:58 AMThis is the perfect opportunity to use a MultiQC plugin or script 🙂
Phil Ewels
09/02/2024, 8:59 AMPhil Ewels
09/02/2024, 9:00 AMShould be possible to run the search + parsing, then add the extra column, then generate a report
Phil Ewels
09/02/2024, 9:00 AMI'm looking for nice examples like these to use in a talk actually 😅
Phil Ewels
09/02/2024, 9:00 AMBig example notebook with various parts of this in a script: https://github.com/MultiQC/example-notebook/blob/master/multiqc_example.ipynb
Phil Ewels
09/02/2024, 9:01 AMDocs for the function to add columns to general stats: https://multiqc.info/docs/development/modules/#step-3---adding-to-the-general-statistics-table
Phil Ewels
09/02/2024, 9:01 AMYou ok to have a go and shout if you need any help?
r
Rike Hanssen
09/02/2024, 9:02 AMamaze thank you! Yes good to go and will shout if I get stuck
p
Phil Ewels
09/02/2024, 9:05 AMawesome
r
Rike Hanssen
09/02/2024, 9:46 AMQuick check on fastp in particular: The
modulefastpfastp-4fastp-5p
Phil Ewels
09/02/2024, 9:48 AMDo you have any config stuff? Running the module multiple times for example?
Phil Ewels
09/02/2024, 9:49 AMBut yeah an example could be nice. @Vlad Savelyev is looking into refactoring how ids / anchors work to avoid exactly this kind of confusion
r
Rike Hanssen
09/02/2024, 9:52 AMno just once. I imported the data from the work directory of the original multiqc run, where I expect the script to later find the data. I just want to be sure the module name is fixed in the end, so I can run this without intervention.
Will test out where the numbers come from
Rike Hanssen
09/02/2024, 10:06 AMok it seems to count up when I re-run the
parse_logsp
Phil Ewels
09/02/2024, 12:52 PMIt's probably because each time you run that it's saving a new copy of the data
Phil Ewels
09/02/2024, 12:52 PMRather than overwriting
r
Rike Hanssen
09/02/2024, 12:59 PMyes, I can see how that makes sense in an interactive mode
👍🏻 1
Rike Hanssen
09/03/2024, 8:51 AMhah this is amazing. thought I had to manually sort all the plots back in, but no they just appear magic
p
Phil Ewels
09/03/2024, 9:01 AMsparkles