Friederike Hanssen

If VEP does not produce output, MultiQC fails

4

### Description of bug Hi! Whenever we use VEP with inproper data, the tool itself runs fine, but produces incorrect output. If it is then passed to MultiQC, it fails....

[Feature Request] Add path autocomplete to parameter tokens

1

Thanks for the nice tool. 🚀 Often I end up having to type in different paths into what is essentially the same command. So basically have the path be a...

Prevent publishing bam2fastq related modules & unnecessary tabix run

1

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

freec ploidy number -> String

1

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

TMB

8

#495 Coming up with a POC for the tmb support: Idea is to keep all relevant config files for the tmb tool in our own assests folder (or any other...

The module `create_intervals_bed` uses `awk` magic to split up interval files into batches of similar genome size. However, for the naming of the file the first interval is being used,...

GA4GH compliant

1

https://www.ga4gh.org/ https://seqera.io/blog/tower-api-docs-release/ More info to follow

Make WARN: Found unexpected parameters more prominent

4

### Description of feature The warning about an unexpected parameters is almost immediately followed by the whole pipeline header about used parameters etc. often leading to it being too fast...

Lint that the same tools use the same container versions

1

### Description of feature Recently encountered in sarek that modules that use the same tool, i.e. MultiQC end up using different containers: ``` quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0 quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1 quay.io/biocontainers/strelka:2.9.10--0 quay.io/biocontainers/strelka:2.9.10--h9ee0642_1 ``` resulting in...

### Description of feature As discussed on [slack](https://nfcore.slack.com/archives/CJRH30T6V/p1646901205199769), it would be great to have some sort of automatic checking for new software releases, replacing the version lines in the module...