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Test data for MultiQC.

Home Page: https://multiqc.info

License: MIT License

CSS 0.05% JavaScript 0.12% HTML 98.67% R 0.01% TeX 0.01% Shell 0.01% Roc 1.17%

multiqc test-data bioinformatics-data bioinformatics

test-data's Introduction

Aggregate bioinformatics results across many samples into a single report

This repository contains files to test MultiQC with. These are used in the automated continous-integration tests and can be used whilst developing for MultiQC.

Contributing

To add new files to this repository, please follow the following procedure:

After forking the repository to your own GitHub account:

git clone <forked-repo-address>
cd <repo-directory>
cp /your/files/. ./data/modules/<module_name>
git add .
git commit -m "<message describing change>"
git push

Create a Pull Request to bring your changes back into this repository.

Delete your fork once the PR is accepted (optional)

For information about MultiQC, please see http://multiqc.info or the main MultiQC GitHub repository.

test-data's People

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lpantano ramaniak roryk hlwiencko robinandeer mgavery hammarn mateongenaert kunzej boulund vladsavelyev leipzig epruesse edinburghgenomics t-neumann bubioinformaticshub alexanderscholz cliu72 astewart-twist vezzi ekopylova tanaes iimog asetgem ehsueh winni2k pzumbo remiolsen dfornika dpryan79 matthdsm parlundin joachimwolff sidbdri amchalkie zwdzwd princessmaximacenter maplesond apeltzer brucemoran ousamg florianduclot nservant oneillkza correyl inambioinfo chuan-wang lucacozzuto manavalang rlegendre barrymoore alneberg jakevc sachalau mticlla elizabethcook21 smeds florianthibord singerj samhunter ssjunnebo claymcleod k-hadidja nh13 felixkrueger elahamer drpatelh joseespinosa jamorrison noirot avsastry mahesh-panchal jfy133 ferreirafm maxibor cerebis bnbowman caspargross abretaud s4hts sstadick redmar-van-den-berg iamh2o tclamnidis kpalin maarten-vd-sande subwaystation will-rowe a-frantz andrei-seleznev ftabaro matthpich erikdanielsson jambler24 vsmalladi kevbrick pichauma maleasy imgag ic-induja

test-data's Issues

Move varianteval output under subfolder

@ewels perhaps you can move the varianteval output under "gatk/varianteval" to follow the samtools, picard example :)

Add testing instructions to the readme

Hi!

I understand this repo contains test data for multiqc. Is there a recommended way of running these tests locally?

Where I'm at:

I've made some changes to multiqc
I want to test them

In multiqc dev docs, I see that github actions will likely run the testdata against my changes to multiqc: https://github.com/ewels/MultiQC/blob/master/.github/CONTRIBUTING.md#review-workflow

But I also want to modify testdata too. I want to add a test and run it against my branch of multiqc. Feels like adding anything in the readme could be helpful!

If I figure something out I'll PR it.

Can't extract Picard CollectRnaSeqMetrics information

Hi Phil,

As we discussed over Gitter, I have trouble to get MultiQC recognize the CollectRnaSeqMetrics results. Please find the attached an example file for you to test. Thanks!

Best regards,
Lei
CTC-1-AA-B2.star.bam.rnaseqmetrics.txt

Tech debt: replace synthetic test data with empirical data for various fgbio tools

See comment: #139 (comment)

Help wanted: interop data

Hi Phil,

I don't know if you've had the time to take a look at the testdata I've submitted, but I'm having some issues parsing it to a suitable json structure.

Can you offer any advice about how to best structure the data dict, so we can get some nice tables?

Thanks
M

example peddy 1kg data

1kg here is the background data for peddy. see brentp/peddy#20
example.background_pca.json.gz

Expose additional statistics in Picard Alignment Summary

The issue

The Picard Alignment Summary currently only shows the number of aligned reads in the barchart. This makes sense for Illumina data, where all reads are the same size. However, for long read sequencing, the number of aligned reads is not so relevant, and the number of aligned bases or the mean read size is more relevant.

The proposal

Add additional datasets to the picard Alignment Summary section. This way, the default behaviour will be the same (show the number of aligned reads), but users can switch over to number of aligned bases or mean read length, if this is more relevant for them.