Refine nf-scil framework

[AlexVCaron]

Some steps must be taken to make nf-scil framework as easy to use as possible :

• Most nf-core modules commands require to add --git-remote and/or --branch even when called from inside nf-scil
  • When inside the nf-scil directory, all commands must refer to nf-scil by default, then to any other library
  • Outside the directory, we should have the same behavior, if able
  • Roadmap :
    • Contact nf-core to discuss what is the best way to get that
    • Implement the modifications required in nf-core/tools and submit them the PR
• The modules and subworkflows templates can be overridden, we need to do this so we only have nf-scil related stuff when we use the create commands
  • Roadmap :
    • Create the required handles in nf-core/tools to make it possible to override the templates
    • Submit it to PR to nf-core
    • Create the templates we need in nf-scil
    • Refine nf-scil documentation
• The development environment is still finicky. We need to stabilize it so our users have a good time creating modules
  • Roadmap :
    • Find how to make docker-outside-of-docker work with our use case. Right now, it doesn't since testing workflows creates data inside the main container, inaccessible to outside ones created by Nextflow to run them.
    • If above is impossible, find a way to remove privileged from the devcontainer, while still using docker-in-docker
    • If all above fail, find a way to keep privileged while fixing files permissions and ownership between the container and the main OS
    • Find how to make the poetry environment correctly loadable by VSCode
• The infrastructure for testing data is still in progress :
  • Roadmap :
    • Implement the DVC framework for test data versioning outside of nf-scil (in the SCIL organization)
    • Bind the DVC framework in nf-scil using modules and subworkflows
    • Change all tests to use DVC and remove .test_data and the Scilpy Fetcher