Singularity fixes

• 1.2.1
  • Patch: Added Singularity.def to be able to create Singularity containers with environment.
  • Patch: Removed process resource settings from nextflow.config because these are anyway taken from the main.nf
  • Patch: Replaced process { ... } blocks in nextflow.config with process.varName references. The former do not combine with multiple profiles, but override.
  • Patch: Bumped minimum Nextflow to 23.10.1. Version 22 uses singularity exec, while 23 uses singularity run, which impacts process isolation.
  • Patch: Change default container name to Nextflow's default for downloading the container.
  • Patch: Updated container image.
  • Patch: Renamed tests/runIntegrationTests to integration-tests/run.sh.

Closes #4

Summary by CodeRabbit

• New Features
  • Added support for Singularity container alongside Docker for workflow execution.
  • Introduced a new workflow section for streamlined data processing in main.nf.
• Enhancements
  • Updated integration test paths and execution procedures to support both Docker and Singularity containers.
  • Enhanced container specifications to improve environment setup and labeling.
• Documentation
  • Updated README.md with instructions on container handling and integration test execution.
• Configuration
  • Updated .gitlab-ci.yml for integration test execution path.
  • Adjusted nextflow.config with version updates and profile configurations for improved compatibility and flexibility.