Brian Fulton-Howard

Problem with N_INFORMATIVE after --impute drop

1

I run the following, expecting missing genotypes to be dropped for any given variant: ```raw ./rvtest --inVcf [file] --impute drop --pheno [pheno file] --pheno-name [pheno] \ --sex --covar [pheno file]...

It appears to be half-closed 1-based. Is that correct?

Cannot retrieve works ("application/json;charset=UTF-8" is not TRUE)

3

Session Info ```r > sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base...

base conda environment not automatically activated by `singularity shell ...` or `singularity exec ...`

9

I want to download and extract a zip file in addition to creating an environment, but I cannot install with apt-get or with mamba. With apt, I get the following...

**Is your feature request related to a problem? Please describe.** If a file may be used after a checkpoint, but is not in the initial DAG, it is deleted once...

LSF executor plugin

17

**Is your feature request related to a problem? Please describe.** It would be nice to have an LSF executor plugin like the `--slurm` executor. **Describe the solution you'd like** I...

Remote modules fail when execution nodes do not have internet

6

**Snakemake version** 7.17.1 **Describe the bug** When using workflow modules that are hosted remotely, the individual cluster execution subprocesses attempt to access environment definitions and potentially scripts, instead of only...

`mem_mb` and `mem_mib` do not match `mem` when `mem` is specified with unit.

4

**Snakemake version** Version 8.9.0 **Describe the bug** When `mem` is specified with a unit, the `mem_mb` and `mem_mib` resources do not make sense. For example, when the request is `mem="2G"`,...

In most tools, ES is treated like a β rather than an odds ratio (OR). Additionally, if an OR is used, the results will be incorrect. Because of this, could...

Continuous covariates

9

### Description of feature Many users including us would like to be able to include continuous covariates for the differential expression tests. They could be added to the contrasts sheet...