Matthew J. Oldach
Matthew J. Oldach
The [`benmarwick/rrtools` package](https://github.com/benmarwick/rrtools) has a function (`rrtools::use_dockerfile`) which creates a dockerfile along with a project template. I'm wondering if a similar function for `starters` would be desired as a function...
When running the two snakemake wrappers `Varscan` -> `SnpEff` in succession there is an error thrown https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876 This does not happen when feeding `Varscan` to the `VEP` annotation tool. This...
**Snakemake version** `5.24.2` **Describe the bug** I'm getting an error when using the `Strelka2` wrapper when using the `--use-singularity` and `--use-conda` commands in conjunction but not when `--use-conda` is used...
**Snakemake version** > 5.8.1 **NOTE:** I will go over why I'm not using the latest version in the **additional context** section **Wrapper version** > 0.64.0/bio/fastqc **Describe the bug** I'm getting...
There are currently two separate wrappers for [SAMTOOLS MPILEUP](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/samtools/mpileup.html) and [VARSCAN MPILEUP2SNP](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/varscan/mpileup2snp.html) These tools are used sequentially and unfortunately **single-threaded**. I'm in the process of converting `shell` commands to `wrappers`...
**Snakemake version** ### `Snakemake` > 5.23.0 ### Wrapper **Issue** I'm trying to adapt my regular VEP code to use the snakemake wrapper instead but am running into an issue. I...
I would like to use `ExpansionHunter` on _C. elegans_ WGS data and I'm wondering if you are aware of a [Variant Catalog (in `JSON` format](https://github.com/Illumina/ExpansionHunter/blob/master/docs/04_VariantCatalogFiles.md) for this model organism? I...
I'm getting an error from bioperl that I don't know how to solve. I assume something with my `bioperl` is broken as this code works on a colleagues ComputeCanada account....
Is it possible to rotate/flip/fop an image with `geom_image()`? I would like to get the mirror-image based on a binary variable. For example, given that `z` is either `"A"` or...
I'm getting an error when trying to look up some functions from the `scater` Bioconductor package. It's giving me an error about `BiocInstaller` which shouldn't be an issue since that's...