Gregor Sturm

### Description of feature If multiple contrasts were run through the pipeline, it would be nice to show an upset plot in the quarto report that shows the overlap of...

Contrasts not being processed with DREAM

1

### Description of the bug When running the pipeline with DREAM, `VARIANCEPARTITION_DREAM` is only executed once, even though there are three contrasts. Even for the one contrast that does get...

Contrast specified with formula does not appear in HTML report

4

### Description of the bug When I specify contrasts like this in a `contrast.yml` file ```yaml contrasts: - id: BORC_simple_PD_vs_SD_formula formula: ~ 0 + BORC_simple make_contrasts_str: "BORC_simplePD - BORC_simpleSD" -...

Option to disable filtering

2

### Description of feature I would like an option to disable filtering altogether. My use-case is that I have data that doesn't fall in the filtering scheme provided by the...

### Description of the bug I don't see a good reason not to allow numeric sample identifiers and I don't think it's that uncommon to have some. Part of the...

### Description of feature It would be great to enable multithreading for methods that support it. It is probably fine to use a moderate number of parallel threads (8-16) by...

### Description of feature Based on the `--filtering_.*` options, features are removed from the input matrix. I believe it would be important to the user to show statistics how many...

### Description of feature Currently we have plots for a dendrogram colored by all covariates. I think it would be more informative, and more compact to reduce this to three...

Improve caching behavior

1

### Description of feature Right now, when I add or remove a contrast, e.g. ```diff contrasts: - id: BORC_simple_PD_vs_SD comparison: ["BORC_simple", "SD", "PD"] - - id: BORC_simple_PD_vs_SD_formula - formula: ~...

### Description of the bug Currently, in the DESeq2 module, the "make_contrast_str" is passed via the `name` parameter to `DESeq2::results` https://github.com/nf-core/differentialabundance/blob/ecfdc89c7ec3cf5404b430d11cc47eed5e8057a2/modules/nf-core/deseq2/differential/templates/deseq2_differential.R#L436-L438 This allows to use one individual coefficient as contrast,...