Code for key analyses in the manuscript Single-nucleus chromatin and gene expression profiling across hundreds of skeletal muscle samples reveals context-specific regulation. Annotations in hg38.

To run workflow:

Specify all paths in config.yaml

Modify scripts/nextflow.config accordingly. It currently provides configuration to run on the slurm scheduler.

To generate the sigularity container, use the Singularity file in the scripts directory to generate one as:

singularity build --remote container_name.sig scripts/Singularity

Run the Nextflow workflow as:

nextflow -C scripts/nextflow.config run scripts/main.nf -params-file config.yaml -resume -with-trace trace.txt