snakemake-wrappers
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snakemake
This is the development home of the Snakemake wrapper repository, see
The contribution docs are currently being extended and improved by @mbhall88 in PR #380. During the review of this process, we re-identified a long standing shortcoming of the contribution docs,...
**Snakemake version** snakemake-wrappers: 0.74.0 **Describe the bug** The [vep download cache](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/vep/cache.html) wrapper uses the vep_install `--AUTO cf` mode, which downloads the cache _and_ fasta data. However, the [vep annotate](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/vep/annotate.html) wrapper...
**Snakemake version** Snakemake wrappers version 0.64.0, Snakemake version any (e.g. 5.26.1) **Describe the bug** FASTA or FASTQ files could be often be named like `*.fq.gz`. Starting from 0.50.0 version fastqc...
**Is your feature request related to a problem? Please describe.** Difficulty developing an assembly benchmarking pipeline due to the dependencies associated with two key bioinformatic tools use in the pipeline...
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...
**Is your feature request related to a problem? Please describe.** @tdayris is currently working on unifying the handling of Java memory specifications in wrappers where the bioconda recipes allow for...
**Snakemake version** Stable release of wrappers - `0.66.0` **Describe the bug** When viewing the documentation on readthedocs, the `stable` tag doesn't show the `code` blocks. Other version tags and the...
Hi, the wrapper for PICARD CREATESEQUENCEDICTIONARY creates an unfinished *.dict file. Do I need to attach any additional parameters for a correct *.dict file? Many thanks. Best regards, Raphael
**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...