Florian Wuennemann

Problem running scde on linux cluster. Fortran "dqrls" not resolved

8

Hi there, I am trying to run SCDE on a Linux computational cluster. I am getting the following error when running on a single core: ``` Error in .Fortran("dqrls", qr...

Issue with singularity when running infer_trajectory

20

Hi, thanks for developing this amazing package and for the incredible amount of work you put into benchmarking all of these tools, a great effort! I was trying to run...

Deploying Docker files on a VM

5

Hi there, thank you very much for developing SCOPE and making it available via so many different ways (macOS, linux, Windows, Docker). I was trying to set up a SCOPE...

Added index and t2g file required for tests of https://github.com/nf-core/modules/pull/409

Issue with saving h5ad file after Convert

1

Hi SeuratDisk developers! Thanks for the package and for all the functions around Seurat, making users life's easier! I was trying to create an anndata file from the rPCA tutorial...

Add stardist 0.8.5 recipe to containers

11

# Submitting a Container (If you're requesting for a new container, please check the procedure described [here](https://github.com/BioContainers/containers#241-how-to-request-a-container). ## Check BioContainers' Dockerfile [specifications](https://github.com/BioContainers/specs) ## Checklist 1. Misc - [x] My tool...

Seurat wrapper not working for Seurat v5 objects

2

**Describe the bug** I am trying to run vitessceR using Seurat v5 objects as input. I get the following error: ``` Warning: Overwriting previous file data/seuratdata/A/0/seurat.zarr.h5Seurat Creating h5Seurat file for...

Gitpod

7

This PR adds a config file for gitpod, which will allow to start a Gitpod instance from the spatialdata container. Currently, this is pointing to a test placeholder container I...

Unicycler nftest

9

## PR checklist Adds nf-test for unicycler module.

Question about naming tool/subtool for nf-core module

7

Hi everyone, as discussed, we want to write the MCMICRO spatialdata-io reader (https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/mcmicro.py) as an [nf-core DSL2 nextflow module](https://github.com/nf-core/modules) that can collect output from MCMICRO at the end of the...