Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Jan 31 2019 16:04
    ewels closed #894
  • Jan 31 2019 16:04
    ewels commented #894
  • Jan 31 2019 15:38
    ewels closed #896
  • Jan 31 2019 15:38

    ewels on master

    Replace inf values with nan in … Update of changelog Merge pull request #896 from al… (compare)

  • Jan 31 2019 15:37
    ewels commented #894
  • Jan 31 2019 15:30
    alneberg edited #896
  • Jan 31 2019 15:28
    alneberg synchronize #896
  • Jan 31 2019 15:20
    alneberg opened #896
  • Jan 31 2019 11:36
    alneberg commented #894
  • Jan 31 2019 08:40
  • Jan 30 2019 17:46

    ewels on master

    Add biobambam2 to config.module… (compare)

  • Jan 30 2019 17:22
    ewels commented #895
  • Jan 30 2019 17:21
    ewels closed #895
  • Jan 30 2019 17:21

    ewels on master

    New module: biobambam2/bamsorma… (compare)

  • Jan 30 2019 16:41
    ewels commented #895
  • Jan 30 2019 12:37
    fgvieira commented #895
  • Jan 30 2019 11:18
    ewels commented #895
  • Jan 30 2019 11:17
    ewels labeled #895
  • Jan 30 2019 11:06
    ewels commented #894
  • Jan 30 2019 10:59
    ewels labeled #894
sophie22
@sophie22
Thank you
Phil Ewels
@ewels
Picard is the exception to the rule in that there are some module specific config options for certain columns: https://multiqc.info/docs/#picard
But not the one you’re looking for I’m afraid
andreamanz
@andreamanz
Thank you Phil, it work! :)
Phil Ewels
@ewels
Hooray! :tada:
apeleraux
@apeleraux
I face an issue using multiQC html reports that have multiple columns in the General Statistics table. When I click on the configure columns button, the pop-up window is too long and I don't have access to the bottom of the list nor to the button to validate my choices. Is there a workaround to avoid this issue? Would it be possible to implement a scroll bar on the right-hand side of this pop-up window to enable scrolling up or down?
apeleraux
@apeleraux
Another issue is that samples have different names depending on the tool that was used to generate the QC. For example, sample SRX2264037 is named SRX2264037.sort, SRX2264037_BAMqc, SRX2264037_hisat2_summaryfile). Hence they appear in 3 separate rows in the General Statistics table, whereas they should be in a single row. I know that there is a way to rename the samples: https://multiqc.info/docs/#bulk-sample-renaming. But I am not sure that this will solve the issue since renaming these 3 samples to SRX2264037 using the MultiQC Toolbox in an existing report is not sufficient to merge the 3 rows in the General Statistic table. Is there another way to achieve this goal?
Phil Ewels
@ewels
Hi @apeleraux - the config window should scroll already (I think it does for me? Maybe I should double check..)
What web browser and operating system are you using?
1 reply
Could you send me an example MultiQC report where it’s not working please?
2 replies
Regarding the second question, you’re looking for sample name cleaning: https://multiqc.info/docs/#sample-name-cleaning
1 reply
Michael Milton
@TMiguelT
Did the format of the multiqc_data.json change at some point between 2018-2019? From one report I have a general stat named FastQC_mqc-generalstats-avg_sequence_length and from another it's called FastQC_mqc-generalstats-fastqc-avg_sequence_length and another it's FastQC_avg_sequence_length-1. So the "generalstats" thing (dis)appeared and so did the "mqc" string perhaps?
Phil Ewels
@ewels
Yes or just drag and drop on to Gitter and it should upload
(Maybe you have to zip it first?)
@TMiguelT - I don’t think so? But those are IDs from the module so possible that they may change
The _1 suffix comes when an ID is not unique so could be when a MultiQC report runs the FastQC module twice
I suspect that the mqc_generalstats thing is because the stat is in twice?
Once from the module and once from the general stats table
If that makes sense
3 replies
Phil Ewels
@ewels
Duplication in the MultiQC report I mean though. As in this: https://multiqc.info/docs/#running-modules-multiple-times
Then the FastQC columns will all be in the general stats table twice
Douwe van der Leest
@ikkextoch
Heya, I'm trying to figure out how to format columns within custom data. My interest is especially with column width and/or centring values. Two of my columns contain genetic positions and one contains genetic strands. The two columns containing numbers are partly overlapping in my output and the strand info is directly adjacent to the number on the second column on my macbook screen. Is there a way to change this?
Phil Ewels
@ewels
Hi @ikkextoch - short answer is no basically I'm afraid
Can you just divide by 1000000 and show the coordinates in megabases instead?
I've deliberately avoided adding the ability to customise things like this as I want MultiQC reports to be as consistent as possible in their output
Also I encourage numbers to use mega- kilo- etc dividers as I think that it makes comparison of values much easier for a reader. eg. 837284 vs 8372845 and 8.37 vs 83.73
Douwe van der Leest
@ikkextoch
Thanks for your answer, I understand you reasoning. In my particular case the goal is not to compare values between sample, but rather to provide data on low coverage baits for WES data. I am sort of feature abusing the multiQC report for this as our current approach of qc checking heavily uses multiQC and the user preferablly doesn't want to view these bed files from the command line or a different tool.
Phil Ewels
@ewels
Yup, understandable. You can always hack it a bit by using custom HTML inside the table with a bit of fidding around
eg. instead of 123456 use <code><small>123456</small></code>
That might help at least. You might also need to turn off some of the automatic formatting / background bar feature stuff
And worst case scenario, you can have sections where you just input whatever raw HTML you want
So you could build your own table from scratch (MultiQC uses bootstrap... 3? so you can use those CSS classes)
Aisha-D
@Aisha-D
Hiya, I'm presenting somalier output file as custom data in the config file however I am having issues forcing it skip the first column. If I read in the second column (which is sample_id) 'col1_header': 'sample_id' , the data doesn't appear in the report. Is it not possible to force the custom data to skip the first column? I'm not using the somalier module as it doesn't include appended columns in the somalier outputs which I need to the MultiQC report to include.
Phil Ewels
@ewels
Hi @Aisha-D - could you perhaps hide the column using the general table config? https://multiqc.info/docs/#hiding-columns
Otherwise I'm afraid you'll need to preprocess the file
Or better still, submit a PR to add your missing functionality to the somalier module :)
MarieLataretu
@MarieLataretu

Hi there, I'm having trouble running QUAST twice. My first step was to run it with a renamed report file full_assembly_report.tsv, instead of report.tsv, but MultiQC doesn't find the file. For fastqc it works perfectly.
My config looks like this:

module_order:    
    - fastqc:
        name: 'FastQC (trimmed)'
        anchor: 'fastqc_trimmed'
        path_filters:
            - '*trimmed_fastqc.zip'   
    - fastp:
        anchor: 'fastp'
    - fastqc:
        name: 'FastQC (raw)'
        anchor: 'fastqc_raw'
        path_filters_exclude:
            - '*trimmed_fastqc.zip'
    - hisat2:
        anchor: 'hisat2'
    - quast:
        name: 'QUAST (full assembly)'
        anchor: 'quast_full'
        path_filters:
            - 'full_assembly_report.tsv'   
    - custom_data

Do I miss something? (The filename is not misspelled and the file is there - I checked that...)

Phil Ewels
@ewels
Path filters only restrict what files have been found by the module. If you want to change the way that the module finds files in the first place you need to customise the module search patterns: https://multiqc.info/docs/#module-search-patterns
You can see that QUAST looks for a file called report.tsv - https://multiqc.info/docs/#quast
So you need to change that too - add to your config something like this:
sp:
  quast:
    fn: 'full_assembly_report.tsv'
(or maybe *report.tsv if you want both reports)
Then once MultiQC is finding all of the Quast outputs you can restrict which ones get to which module_order version of quast via the path_filters
Make sense?
MarieLataretu
@MarieLataretu

Aha, yes it totally makes sense!
With this:

module_order:
    - quast:
        name: 'QUAST (full assembly)'
        anchor: 'quast_full'
        path_filters:
            - 'full_assembly_report.tsv'  

sp:
  quast:
    fn: '*report.tsv'

MultiQC finds the file, but it cannot match the path filters:

[2021-02-26 22:48:58,783] multiqc.modules.base_module                        [DEBUG  ]  quast - Skipping 'full_assembly_report.tsv' as it didn't match the path_filters for 'QUAST (full assembly)'

Any idea?

Phil Ewels
@ewels
Sorry on my phone now (done for the weekend) and can’t see the full log.
Missing the * on the path filters maybe?
If it’s the full path with directories you may need that
I forget exactly how that works off the top of my head
MarieLataretu
@MarieLataretu
Yes, thank you! '*full_assembly_report.tsv' for the path filter works!
Enjoy the weekend! :)
Phil Ewels
@ewels
:tada: