Hi everyone!
I'm planning to integrate two additional tools into rnasplice: IRFinder-S and MAJIQ. I've already implemented both in my own Nextflow pipeline, but I'd appreciate some guidance on how best to turn these into nf-core modules, particularly regarding dependencies and CI testing.
Both tools come with a few challenges:
IRFinder-S:
• Not available on Conda, but the developers provide a working public Docker image.
• Has a hardcoded minimum RAM requirement of 32 GB, which prevents it from running on standard GitHub Actions runners.
MAJIQ:
• Not available on Conda, and there is no official public container image.
• Can be installed from its GitHub repository. In my current implementation, I build a custom Docker image in CI before running the pipeline.
• Requires a license, which I currently handle using Nextflow secrets.
Both tools are already working in my pipeline, which you can find here:
github.com/ZarnackGroup/majiq_splicing_analysis_pipeline/tree/main
I'm mainly wondering what the recommended nf-core approach would be for creating modules for these tools and handling their CI tests, given these limitations.
Any advice on how best to proceed would be much appreciated!