FASTQE

[adamrtalbot]

Name of the tool

fastqe

Tool homepage

https://github.com/fastqe/fastqe

Tool description

Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason.

Tool output

fastqe.zip

Log filename pattern

No response

Data suitable for MultiQC plot(s)

No response

Most interesting data for the General Stats table

An average quality score. Represented as an emoji.

Before submitting

• I have included example data (zipped, not pasted) that can be used to write the module.

[lonsbio]

Can I just say it would be a dream come true to have fastqe in MultiQC, thank you! Please reach out if there is anything I can do to help on the fastqe side to make this easier.

A long long time ago @ewels advised about direct html import as way to do it. An alternative HTML output format using --html option in fastqe 0.3.1 onwards was designed for Galaxy integration but with MultiQC in the back of my mind. I have run a POC with that at some point to get MultiQC to pick it up.

That report is still a little clunky though and hard to customise, so I fully support this approach of using the text emoji output for MultiQC.

Again, happy to help if need be!

[lonsbio]

This is what the POC looked like with an experimental --html report

It might not be for everyone though, and there's a few outstanding issues with the HTML report, but might be an option to add later on.

[adamrtalbot]

Nice, that's great to hear. I've added the corresponding nf-core module here and started implementing it into nf-core/seqinspector here. This is the final piece of the puzzle.

@edmundmiller started an attempt here in between sessions at the Nextflow summit: #2945

[ewels]

x-link my ancient issue on the topic: fastqe/fastqe#11