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nf-core / demultiplex

Demultiplexing pipeline for sequencing data
https://nf-co.re/demultiplex
MIT License
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Documentation and file type for SampleSheet.csv #90

Open mschubert opened 1 year ago

mschubert commented 1 year ago

Description of feature

This is related to https://github.com/nf-core/demultiplex/issues/81, which states (but is not the main concern of the linked issue)

Also https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/MiSeq/SampleSheet.csv doesn't seem like proper csv to me.

Would it be possible to add some documentation on how to write such a SampleSheet.csv file, and (probably) fix the extension to TOML?

I tried to look for it on https://nf-co.re/demultiplex/1.1.0/usage, but there was no mention of this.

edmundmiller commented 1 year ago

Is it a TOML though?

mschubert commented 1 year ago

Well, also not really. Hence the probably and the question mark.

But the more important part is that reading the usage documentation, I've got no idea how to write such a file. To get some more info there would be great!

Btw, great that you're maintaining this pipeline! :+1: I'd love to use it.

edmundmiller commented 1 year ago

It's an Illumina "Samplesheet" https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/BCLConvert/SampleSheets_swBCL.htm

So I think linking to those docs would solve this.