Friederike Hanssen

Segmentation fault version 1.3.0

13

Hi, I am running dragmap 1.3.0 on some small test data and continue to get a failure with ``` 0 Segmentation fault dragen-os -r dragmap --num-threads 2 -1 test_1.fastq.gz -2...

### Description of feature as the title says, using fetchngs directly with sarek would be super convenient.

CRAM as input format?

4

I was wondering whether `cram` is also an accepted input format. I can't get FastQc to run with it, but I was not sure whether the file is corrupted or...

Make available via Bioconda

2

Hi! Would it be possible to make this tool available via bioconda for easier installation and automatic containerization via biocontainers? Cheers, Rike

Question: Multiple samples in a plot

1

Hi, Thanks for this great tool :) is it possible to plot multiple samples in the same plot (for example the histogramm for VAF) either by merging all samples before...

Add highlevel steps to README

1

It would be great if the readme could get a highlevel overview of the pipeline by describing the major steps + a visual overview

- [ ] Adding content on custom modules (@RaqManzano ) - [ ] Figure out what content should be hidden (@mahesh-panchal ) - [ ] Where should exercises go (@FranBonath...

Varlociraptor calls

2

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

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

The pipeline should fail early when --no_intervals is used with joint germline calling

4

### Description of the bug As title states, we used to have it but apparently not anymore, see here: https://nfcore.slack.com/archives/CGFUX04HZ/p1697021363120009 ### Command used and terminal output _No response_ ### Relevant...