Suzanne Jin

We have already implemented the handling of paramsheet in #443. Here we need to enable and fix all the details needed to run multiple configs at one run.

Automatic build of gene set database

2

# Why and goal Currently, if one wants to run functional analysis, the pipeline expects the user to give a gene set file as input. It would be nice to...

- [ ] Update documentation to be less RNAseq centric and possibly - [ ] move RNAseq explanation to a tutorial - [ ] Create tutorial for ATACseq - [...

issues with gprofiler2/gost

3

### Have you checked the docs? - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug Several issues found for module gprofiler2/gost: 1. Inconcistency between...

Currently most modules use `tag $meta.id` but this does not account for the paramset. It would be great to print id + paramset name when running the pipeline.

We have functions like `prepareModuleInput` and `prepareModuleOutput` that are not in `lib`. It would be nice to move them into `lib` as recommended in [strict syntax](https://www.nextflow.io/docs/latest/strict-syntax.html)

Currently, we have defined these parameters in multiple places: nextflow.config, profile, differential subworkflow etc. This should be better coordinated. Also, these parameters should not be exposed to the user (it...

unification of paramsheet and profile

14

### Description of feature With the implementation of the multi-config paramsheet in #423 #422 #464, the profiles such as rnaseq, affy, etc become redundant. Also, it might be confusing to...

bug with contrast parsing?

3

Currently the pipeline creates a `ch_contrasts` for complex contrasts with empty variable, etc: ``` [id:treatment_plus_genotype, variable:, reference:, target:, blocking:, formula:~ treatment + genotype, make_contrasts_str:treatmentTreated] ``` Is this intended? If not,...