A web application to collect and visualise data from multiple MultiQC reports. https://github.com/ewels/MegaQC
in
multiqc_data/multiqc_data.json
"multiqc_bamtools_stats": {
"CEG99-707-64IC_S64_L00.bml.GRCh38.karyo": {
"mapped_reads": 50568874.0,
"mapped_reads_pct": 99.6749,
rather, the sample name is the key of the list of key-values for bamtools_stats
That's probably what's confusing MegaQC
I was hoping that I'd mapped that to something that could be filtered for in MegaQC
but it's entirely possible that I never did
Another question: if I create a .csv or .tsv file with a bunch of metrics and name it with the suffix that MultiQC picks up, will they be in the .json and therefore in MegaQC?
I have done this in the past by adding
_mqc.tsv to the file name
one feature that I would like to add and haven't is the option of having content in such files that is "silent" - that is, that never makes it in to MultiQC reports, but that would then be fed in to MegaQC.
Our use case for this would be to pass metadata from our LIMS through MultiQC and on to MegaQC, without ever printing it in the reports which are sent to users
In this way, MultiQC becomes a kind of normalisation filter for multiple infrastructure back-ends
(by accident)
It does give me though this message:
Finished writing plot data (0 cfg, 164 data points) for report 22
which makes me think I need to add something to instruct how I want each field plotted. Any ideas how @ewels ?
foo name
1 sample1
2 sample2
3 sample3
4 sample4
5 sample5
6 sample6
7 sample7
8 sample8
9 sample9
10 sample10
Do I need to add a config section somewhere so that
foo becomes available to the list of metrics in MegaQC?
Ok, forgot what I said, it turns out the
_mqc.tsv files are loaded into the .html report but are not found in the .json
So I will have to find a way to craft the .json file from the .tsv directly
I'm quite surprised if that's the case
I just doublechecked with some custom content files at my end and it worked ifne
{
"report_general_stats_headers": [],
"config_version": "1.8.dev0 (ef579dc)",
"report_general_stats_data": [],
"config_creation_date": "2019-03-07, 17:42",
"config_title": null,
"config_report_comment": null,
"config_short_version": "1.8.dev0",
"config_intro_text": null,
"report_saved_raw_data": {
"multiqc_my_section_with_a_table": {
"samp_1": {
"col1": 12.523,
"col2": 34.0
},
"samp_2": {
"col1": 56.947,
"col2": 78.0
}
}
},
"report_data_sources": {},
"report_multiqc_command": "/Users/ewels/miniconda2/envs/work/bin/multiqc -f table_headers_mqc.txt",
"config_analysis_dir": [
"table_headers_mqc.txt"
],
"config_report_header_info": null,
"config_analysis_dir_abs": [
"/Users/ewels/GitHub/MultiQC_TestData/data/custom_content/embedded_config/table_headers_mqc.txt"
],
"config_subtitle": null,
"report_plot_data": {},
"config_script_path": "/Users/ewels/GitHub/MultiQC/multiqc/utils",
"config_git_hash": "ef579dcdcdb12a56ea516b2354472cb5f640353c"
}avilella@avilellaM710t:~/multiqc/test$ find $PWD/ -name "*.json" | xargs cat
{
"report_general_stats_headers": [],
"config_version": "1.5dev",
"report_general_stats_data": [],
"config_creation_date": "2019-03-07, 16:48",
"config_title": null,
"config_report_comment": null,
"config_short_version": "1.5dev",
"config_intro_text": null,
"report_saved_raw_data": {},
"report_data_sources": {},
"report_multiqc_command": "/usr/local/bin/multiqc --force --filename /home/avilella/multiqc/test/report__multiqc /home/avilella/multiqc/test",
"config_analysis_dir": [
"/home/avilella/multiqc/test"
],
"config_report_header_info": null,
"config_analysis_dir_abs": [
"/home/avilella/multiqc/test"
],
"config_subtitle": null,
"report_plot_data": {},
"config_script_path": "/usr/local/lib/python2.7/dist-packages/multiqc/utils",
"config_git_hash": null
}
avilella@avilellaM710t:~/multiqc/test$ cat *.txt
# plot_type: 'table'
# section_name: 'My section with a table'
# description: 'a custom text introduction (a few sentences) for this section'
# pconfig:
# namespace: 'Cust Data'
# headers:
# col1:
# title: 'My Column'
# description: 'This is a longer hover text for my column'
# format: '{:,.0f}'
# col2:
# title: 'Second Column'
# description: 'Hover description text'
Sample col1 col2
samp_1 12.523 34
samp_2 56.947 78
avilella@avilellaM710t:~/multiqc/test$ #/usr/local/bin/multiqc --force --filename /home/avilella/multiqc/test/report__multiqc /home/avilella/multiqc/test
that's pretty old
we're on 1.8dev now
My guess is that you need to update MultiQC for this to work with custom content then
Hi Phil,
I am testing the megaqc upload function (locally on my laptop) to get data into megaQC server.
I am getting Error - This function requires MultiQC to be installed..
Following this issue on github https://github.com/ewels/MegaQC/issues/66, I have multiqc installed on my laptop and I am running the upload command from the same environment where I used multiqc to generate the report/json file.
For context, I installed multiqc via conda. The multiqc conda environment is also active in my session. Trying from multiqc.utils import config as multiqc_config on python interpreter also works fine..
Any idea what could be the underlying issue?
Are you super-sure that everything is definitely in the same environment? By checking
which megaqc and which multiqc..?
Ah, and it’s definitely a recent version of MultiQC?
The code that triggers that message isn’t doing anything particularly special: https://github.com/ewels/MegaQC/blob/master/megaqc/commands.py#L173
Ah, that’s going to be interesting.
which multiqc > /Users/kanwals/miniconda3/envs/multiqc/bin/multiqcwhich megaqc > /Users/Kanwals/miniconda3/bin//megaqc
As you can tell, I installed both tools in separate conda environment. Aslo, used pip for megaqc installation.
Should I try installing megaqc in multiqc environment.?
Multiqc version is 1.7, so should definitely be not an issue.