snakemake-wrappers

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### Description This PR adds a wrapper for [pcaExplorer](https://www.bioconductor.org/packages/release/bioc/vignettes/pcaExplorer/inst/doc/pcaExplorer.html#pcaExplorer_User_Guide)'s `pcaplot` function. ### QC * [X] I confirm that: For all wrappers added by this PR, * there is a test...

tdayris

fix: name of bamqc

6

### Description The subcommand name was wrong in the description. Additionally add a region param fro target analyse. ### QC * [x] I confirm that: For all wrappers added by...

christopher-schroeder

feat: Add configurable protocol support to ensembl reference download

8

This PR adds support for configurable protocol, ftp, http, or https to ensembl reference data download and vep cache download. I was evaluating snakemake-wrapper and widely used workflows as a...

pettyalex

Describe in the documentation of STAR wrapper how to use shared memory

2

I know that shared memory can be used in combination with STAR wrapper, as described here #420. But I no not know how to do that. Unfortunately also the documentation...

moxgreen

feat: new inphared-db wrapper

3

### Description Adding a new wrapper to download the current inphared database. ### QC * [ ] I confirm that: For all wrappers added by this PR, * there is...

nacnoriko

feat: add wrapper for rbt vcf_fix_iupac_alleles

4

### 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

Issue with TrimmomaticPE log reporting; incompatible with MultiQC

10

**Snakemake version** snakemake v7.18.2 snakemake-wrapper-utils v0.5.0 **Describe the bug** When using the TrimmomaticPE wrapper (v1.19.2; `v1.19.2/bio/trimmomatic/pe`), I noticed an issue with the log reporting. Instead of listing the actual file...

oligomyeggo

bwa-memx_index meme wrapper expects specific file name?

5

From what I can tell, the wrapper bwa-memx/index in case of bwa=bwa-meme expects one of the output to be named exactly as {input[0]}.suffixarray_uint64. This file is produced by the first...

Phlya

change to earlier docs versions on readthedocs

4

Hello, with the change to the new layout it's not possible to change to an earlier version of the wrappers, or at least I can't find it anymore. Could you...

nnneeennn

`deepvariant`: conda environment not installable

1

**Snakemake version** - snakemake: 7.32.4 - snakemake_warppers: master/v2.9.1 **Describe the bug** Currently the conda environment associdated with the `deepvariant` wrapper cannot be installed. **Logs** ``` (snakemake) xxxx:~/Git/snakemake-wrappers/bio/deepvariant/test$ snakemake -c 6...

votti