Christian Arnold

Error in valid.viewport: 'x', 'y', 'width', and 'height' must all be units of length 1

6

Hi, with R 3.6 I get the following error when plotting two ggplots for patchwork 1.1.1: `g1 | g2 Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale,...

Check rule-specific references also in dryrun

1

**Snakemake version** 7.8, and all versions before **Describe the bug** The dryrun should also catch, if possible, rule-specific errors such as referencing {input.bam} in other rule sections(message, or shell) when...

singularity statement from parent rule ignored for rule inheritance

1

Is it intentional that for rule inheritance, a singularity statement from the parent rule is ignored in the rule that inherits? It seems you have to copy and paste the...

Improve parser error messages

3

**Snakemake version** all **Describe the bug** I receive the following error upon starting Snakemake for a Snakefile: `TokenError: ('EOF in multi-line statement', (257, 0)) ` Very hard to debug, not...

What is the recommended approach to incorporate sample metadata into calculating deviations or subsequently transforming "raw" deviation to corrected ones to remove batch effects etc? At which step can this...

Peak width and resizing peaks, bulk ATAC-Seq data, and other small issues

2

Hi, first thanks for the package, it seems to work nicely. I however have a couple of questions that I think can be clarified in the Docs or somewhere else:...

Low alignment rate even though STAR aligns almost all reads

17

Hi, we are facing the following problem with kallisto 0.44 for paired-end data, but it does not seem to be specific to being paired-end (see below): - [quant] processed 56,725,603...

Snakemake max_version and version in addition to min_version

4

I am suggesting to introduce two more functions in the Utils library that define version and max_version, to precisely specify the wanted snakemake version. With the Singularity bug, I need...

Job names in slurm mode too cryptic

9

**Snakemake version** newest as of today **Describe the bug** When using --slurm, job names are hashes or similarly cryptic characters that make it hard to understand what is running, like...

Error when subsetting or when running other functions: value' must be a 'matrix' or 'dgCMatrix'

18

This issue still exists despite two Issues with the same topic being prematurely closed (#7100 and #7208) Happens with the newest Seurat v5 and a Seurat object that has been...