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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
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Generate samplesheet for nf-core/mag #449

Open CarsonJM opened 9 months ago

CarsonJM commented 9 months ago

Description of feature

Add option to automatically generate a samplesheet than can be input into nf-core/mag

lborcard commented 8 months ago

from which original format you would like to implement that?

jfy133 commented 8 months ago

The idea is to make a samplesheet with the 'processed reads' (e.g, clipped and filtered), so you can skip those sections of the mag pipeline.

@CarsonJM isnl doing something similar on mag for phageanotator if you're interested?

jfy133 commented 8 months ago

Here: https://github.com/nf-core/mag/pull/543

There is a lot of extra stuff in that PR, but the thing is the subworkflow itself.

Maybe @sofstam and @LilyAnderssonLee can orient you if you're interested? I'm working on something else this Hackathon

CarsonJM commented 8 months ago

I'll be into work shortly and am more than happy to help out!