In the EGAPx v0.5.2 release, there is an update to the configuration of resource allocation when executing the pipeline. Please visit the documentation on EGAPx configuration (https://github.com/ncbi/egapx#executors-memory-and-CPU-configuration).

Users running EGAPx in the same working directory used for a previous release of EGAPx may run into issues. Running egapx.py for the first time generates configuration files in the egapx_config folder, which often need to be customized for user's individual compute environments. When egapx.py v0.5.2 is run from that same directory, the configuration files are not automatically overwritten.

Following these steps will re-configure your run environment for EGAPx v0.5.2

1. If configuring with the EGAPx SIF (offline mode), do the following:

rm egap*sif
singularity cache clean
singularity pull docker://ncbi/egapx:0.5.2

2. In the directory where you run egapx.py, remove the .nextflow/ dir
3. Also remove the egapx_config dir (but make sure to save your egapx_config/*.config file for your chosen executor in a separate location so you can copy over custom config options)
4. Re-run egapx.py using the small test data to set up the run, generates egapx_config dir anew
5. Add any needed customization to egapx_config/*.config for your chosen executor and egapx_config/process_resources.config
6. Re-run egapx.py which should start the pipeline