A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello everyone! I think this might be relevant for anyone who is developing pipelines and uses AnnData objects.

Hi all! I (together with ChatGPT) built a <https://github.com/cellgeni/h5ad-cli/tree/main|small CLI> for working with `.h5ad` files. It streams data from disk and processes in chunks, so no need to create an interactive job or worry about crushing a head node.

Here is a list of available commands:
```info     Show high-level information about the .h5ad file.                                                                                                                                      
subset   Subset an h5ad by obs and/or var names.                                                                                                                                                
export   Export objects from h5ad files.                                                                                                                                                        import   Import objects into h5ad files.  ```
Try out on your favorite `.h5ad`
```h5ad info path/to/your/favorite.h5ad```
*P.S.* Check <https://github.com/cellgeni/h5ad-cli/blob/main/docs/GET_STARTED.md|this> for a quick tutorial