Switch to a CSV/TSV based input about exoseq

[marchoeppner]

My vote goes to the "Sarek" approach; should be fairly straight-forward to just steal the code ;)

[apeltzer]

Same here

[ewels]

Or a nextflow params file? nextflow-io/nextflow#208

CSV/TSV is nice and may be necessary here, but I'm also keen for nf-core pipelines to work with minimal input if possible. eg. Still working for someone who turns up with "I have a bunch of FastQ files and know nothing about them." If the pipeline fails because the user doesn't know the platform_model then that's not ideal.

Of course - that's not to say that it's not possible to have both, that would be ideal. Work with minimal requirements but also nice verbose well organised meta files.

[marchoeppner]

For these cases, we actually use this (pardon the crummy'ness of the code):

https://git.ikmb.uni-kiel.de/bfx-core/NF-diagnostics-exome/blob/master/bin/samplesheet_from_folder.rb

Builds a valid input CSV from a folder full of FastQs with actual values where extractable from the fastq files and place holders / best guesses for the other fields. This way you could at least nudge people towards better record keeping ;)

But two mutually exclusive input channels might also work.

[maxulysse]

We have a similar idea that we use for germline sample:
https://github.com/SciLifeLab/Sarek/blob/master/main.nf#L738-L766

[ewels]

Nice! I guess we could embed such a script into the workflow so that it works with a glob of FastQs or a CSV file..? That would be ideal.