Nextflow

[dimalvovs]

This pull request introduces several improvements and new features to the Nextflow pipeline, particularly enhancing parameter handling, reproducibility, and support for additional execution environments. The most significant updates are the addition of new parameters (such as seed and asynchronous_updates), improved output of run parameters for reproducibility, and expanded configuration profiles for various compute environments.

Parameter and Workflow Enhancements:

• Added new parameters to params and workflow logic, including seed and asynchronous_updates, and ensured these are passed through channels and into the COGAPS process for more flexible and reproducible execution. [1] [2]
• Modified the COGAPS process to use the seed parameter and support asynchronousUpdates in the R script, improving run reproducibility and enabling new algorithmic features. [1] [2]

Output and Reproducibility Improvements:

• The pipeline now outputs a params.yml file for each run, capturing all parameters used, which aids in reproducibility and record keeping. [1] [2]

Dependency and Environment Updates:

• Updated the Dockerfile to explicitly install the sparseMatrixStats R package, ensuring compatibility with the Nextflow module.

Configuration and Resource Management:

• Added and refined execution profiles in nextflow.config for different environments (e.g., jhpce, jhu_discovery, igs), with appropriate resource and queue settings for each.
• Adjusted resource allocation logic, including changing the number of CPUs for high-memory processes and correcting the syntax for resourceLimits. [1] [2]

These changes collectively improve the flexibility, reproducibility, and portability of the pipeline across different computing environments.