snakemake-wrappers

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### Description This PR adds a wrapper for GATK DepthOfCoverage tool. ### QC For all wrappers added by this PR, I made sure that * [x] there is a test...

ljmesi

### Description ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and...

fgvieira

### Description A wrapper for datavzrd ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced...

FelixMoelder

fix: fixed GATK3 conda channel priorities and code reformat

5

### Description Fixed conda channel priorities, plus some code clean-up ### QC * [x] I confirm that: For all wrappers added by this PR, * there is a test case...

fgvieira

feat: BWA mem2 index - remove prefix parameter and determine prefix from output

2

### Description Remove the param prefix and detect prefix by output ### QC For all wrappers added by this PR, I made sure that * [x] there is a test...

christopher-schroeder

### Description This PR handles bed intervals, germline vcf, panel of normals input files and f1r2 output file. I also introduced how to enable multi threading in some special cases,...

tdayris

feat: genefuse wrapper

1

### Description Wrapper used to run genefuse ### QC For all wrappers added by this PR, I made sure that * [x] there is a test case which covers any...

Smeds

Update wrapper documentation

6

### Description General `meta.yaml` updates: * no information lost : it has been moved to correct section * no wrapper update: Only `meta.yaml` were updated * key-word arguments provided in...

tdayris

Add GATK ValidateVariants

2

### Description An implementation of the GATK ValidateVariants tool ### QC For all wrappers added by this PR, I made sure that * [x] there is a test case which...

G-kodes

Add cosmic database download wrapper

6

This PR adds a wrapper for downloading files from [COSMIC](https://cancer.sanger.ac.uk/cosmic/download). It expects the following parameters to be set: - `build` (at the moment either "GRCh37" or "GRCh38") - `dataset` (at...

tedil