Matthias De Smet

Could you also add a small readme describing the workflow steps in a diagram? https://mermaid-js.github.io/mermaid/#/ https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

A readme.md file next to `main.nf` seems allright 🤷🏻‍♂️ @Emiller88 , opinion?

Hi @priyanka-surana If you put the flowchart code inside a code block with the `mermaid` designator, it will automatically be rendered. so use ``` \```mermaid \ flowchart TD \ ......

Love it, just left one small comment

@maxulysse , which one is the meta workflow with the aligners?

needs fixin' - [x] applybqsr (invald input) - [x] applybsqrspark (invald input) - [x] calculatecontamination - [x] createsomaticpanelofnormals - [x] filtermutectcalls - [x] genomicsdbimport - [x] getpileupsummaries `A USER ERROR...

@nf-core/core, the CI tests keep failing due to GHA being unable to fetch one file or another from the test-data repo. I'm having the same issues when testing locally. I...

I've no idea, why this happens... I'm regenerating the checksum but get no differences

CI still failing because of subworkflows - [ ] gatk_tumor_normal_somatic_variant_calling - [ ] gatk_create_som_pon - [ ] gatk_tumor_only_somatic_variant_calling

The offending subworkflows seem to be legacy cases with a bunch of wrong inputs. I've no experience with the tools, so I don't intend to try and fix them here....