Gregor Sturm

### Description of the bug When I run the `dev` version of the pipeline with ``` --immunedeconv_run true \ --immunedeconv_method mcp_counter \ --features_id_col gene_id \ --features_name_col GENESMBL \ ``` it...

Simplify pipeline parameters

3

### Description of feature This pipeline has an enormous number of parameters. Each of them creates a maintenance burden (keeping docs up-to-date, take params into account during modifications) and make...

Meta issue HTML report improvements

1

### Description of feature With the toolsheet support (#385) and support for arbitrary contrasts (#362) two major changes are underway in `dev` that will require to update and streamline the...

### Description of feature Meta issue to track improvements to documentation required for 2.0 release

### Description of the bug When the SHINYNGS_APP process gets executed, the warning ``` WARN: Cannot serialize context map. Cause: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue --...

### Description of feature [--size_factors_from_controls](https://nf-co.re/differentialabundance/dev/parameters/#sizefactors_from_controls) and `--control_features` is listed under `[base]` in the parameter documentation, which suggests it's supported by all methods. I'm not entirly sure, but I don't think...

### Description of feature I think it is confusing to have two parameters (`--contrasts` and `--contrasts_yml`) to specify the same thing in different formats. I think we should either *...

### Description of feature I saw that immundeconv is treated special compared to other functional analysis methods: https://github.com/nf-core/differentialabundance/blob/a9e97d0dc8a17dad046c09274b8290a316b5af31/nextflow.config#L140-L143 Potentially, it could become just another parameter for `functional_method` that can be...

v2.0 release plan

2

### Description of feature Hi @pinin4fjords and @suzannejin, do we have a roadmap for releasing the changes that are now in dev? There's obviously still a lot of things that...

### Description of feature linear models allow to test for any of multiple variables being different, equivalent to the classical ANOVA. In limma, this is possible by specifying a list...