#multiqc — Public Fediverse posts

https://seqera.io/multiqc_config_wizard

#MultiQC Configuration Wizard

"this tool helps you create a custom multiqc_config.yaml configuration file. Edit the form on the left, or paste an existing config into the editor on the right. Each option is checked against the schema; status badges and filters let you narrow in on what's set, broken, or unrecognised. "

#bioinformatics

RE: https://mstdn.science/@multiqc/116602059486637406

Had a lot of fun hacking with this over the past few days (it went through multiple variations!)

Thanks to Vlad for doing the initial refactoring work under the hood in #MultiQC and wiring up Pydantic, and starting the first version of config wizard 🎉

Another quality of life improvement is that we now have a #JSONschema via @pydantic for #MultiQC configuration files 🎉

This has been added to schemastore.org so that config files in #VSCode & other IDEs automatically get integrated error checking as you type, see https://docs.seqera.io/multiqc/getting_started/config#json-schema-validation

Did you see, #MultiQC v1.28 went out a few days ago!

There are a handful of release highlights for this version, but perhaps the most exciting is that .gif, .webp and .tiff files are now supported for #CustomContent - you can finally put your favourite gifs into reports! Just name them *_mqc.gif

We're really excited to hear what folks make of the new #MultiQC functionality. Give it a try now with v1.27 and check out the documentation at https://docs.seqera.io/multiqc/ai

https://github.com/MultiQC/MultiQC/releases/tag/v1.27

MultiQC v1.27 was released yesterday. It includes one major new feature:

=== ✨ AI summaries ✨ ===

LLMs are a natural next step for helping scientists understand large datasets. @multiqc now has built-in integration with #Seqera AI as well as #OpenAI and #AnthropicAI 🤖

The premise is fairly simple:
#MultiQC builds prompts with sample data and sends these to LLMs to get summaries.

This can be done at report-generation time and also *interactively* on-demand when reading the report.

And finally a bunch of core improvements! #Python 3.13 now officially supported, and 3.8 dropped. Tooltips, improved memory efficiency, properly sorted samples and strings, default settings for @cursor_ai editor and more!

https://github.com/MultiQC/MultiQC/releases/tag/v1.26

#multiqc #release #bioinformatics #reporting #analytics

#multiqc PR accepted for telseq " a software that estimates telomere length from whole genome sequencing data" ! 🥳 https://github.com/MultiQC/MultiQC/pull/2910

It looks like #multiqc exports TSV files as UTF-8-BOM (byte order mark) https://community.seqera.io/t/unicode-characters-utf8-bom-in-tsv-export-samtools-flagstat-dp-tsv/1502

I cannot read this tsv in #RStats , the columns are shifted. I tried:

read.csv("samtools-flagstat-dp.tsv", header = TRUE, sep="\t", fileEncoding = "UTF-8-BOM")

#multiqc "MultiQC: Grouped samples and custom scripts" https://seqera.io/blog/multiqc-grouped-samples/ #bioinformatics

What I learned today: custom content files for #multiqc are additive . For example if you have two json/barplot with the same section_id but not the same "key", they will be merged in the same plot in the final report .

Dear #lazyweb : this is a #multiqc beeswarm custom plot . What is the config I should use in my mqc.json file, so all the tracks use the same horizontal scale ? #bioinformatics

EDIT: asked https://community.seqera.io/t/custom-content-beeswarm-same-min-max-for-all-tracks/955

using #MultiQC version 1.22.3

Are boxplots supported in custom content ? https://multiqc.info/docs/custom_content/

I tried plotype= box, boxplot, box.plot but I got custom content plot type 'xxxx' not recognised for content ID

I feel very lucky that @SeqeraLabs agreed to take on the @MultiQC project when I joined, so that it can continue to grow and help the bioinformatics / scientific community 🧬🎉📈
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RT @SeqeraLabs
Genomic data management can be a challenge, but with #MultiQC, it doesn't have to be.

This open-source tool, with '000s of users, helps researchers quickly and easily assess the quality of their genomics data across multiple samples 🧬💻

Lea…
https://twitter.com/SeqeraLabs/status/1633415167361916929