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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
The text was updated successfully, but these errors were encountered:
Some steps must be taken to make nf-scil framework as easy to use as possible :
privileged
from the devcontainer, while still using docker-in-dockerprivileged
while fixing files permissions and ownership between the container and the main OSThe text was updated successfully, but these errors were encountered: