Suzanne Jin

Hello @grst! Thank you for proposing this! It looks good to me. Just one comment... is it possible to do something like this if required? ``` - id: treatment_a_vs_b_vs_c type:...

@grst Sure! The flexibility to accomodate different ways could be nice. In the specific case I was mentioning above is more for all against all. It was just to mention...

> > as it asks a slightly different question: is a gene changing across the different conditions. > > so basically the ANOVA case? yes exactly!

> Regarding the "Toolsheet", how does that relate to what we proposed in [#362](https://github.com/nf-core/differentialabundance/issues/362)? The toolsheet is to decide which DE and functional analysis methods to run. An example is...

> I'm wondering if it wouldn't be more convenient to specify everything in yaml format? I don't have too much of a strong feeling between yaml or csv format. However,...

> What are the implications of this? Would you fail the pipeline if a user specifies an "invalid" combination? Don't have a plan for that yet, but one option is...

> I'm also afraid that all the parameters for a differentialabundance run get scattered across too many places... nextflow params, contrasts file, toolsheet file, samplesheet... I'd rather reduce the number...

> Just to clarify again, this will _only_ be in the pipeline and the user specifies the combination of tools using standard params, e.g. `--pathway deseq2_gsea,limma_gprofiler2`? Or will this be...

Here I created a meta issue with all the steps/sub-issues needed to achieve what we agreed to do. Let me know what you think and if you would add/modify anything...

> I'm wondering if it wouldn't be more convenient to specify everything in yaml format? > Actually @mirpedrol , if it is in yaml format, does it mean that it...