Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add workflow.nf for DELLY and BCFtools #81

Open
Faizal-Eeman opened this issue Nov 8, 2022 · 1 comment
Open

Add workflow.nf for DELLY and BCFtools #81

Faizal-Eeman opened this issue Nov 8, 2022 · 1 comment
Assignees
Labels
enhancement New feature or request

Comments

@Faizal-Eeman
Copy link
Contributor

    `workflow-tool.nf` and `tool.nf` are different.  `tool.nf` has all the processes. `workflow-tool.nf` has a workflow that calls all the process. See examples here: https://github.com/uclahs-cds/pipeline-call-gSNP/tree/main/module

Originally posted by @maotian06 in #76 (comment)

@Faizal-Eeman
Copy link
Contributor Author

Faizal-Eeman commented Nov 8, 2022

#76 (comment)

Generally, that's true though we don't necessarily have a formal guideline about this. We try to modularize processes and then create separate workflows (ex. call-gSNP has some core processes that are then used by the various workflows like single-sample mode, multi-sample mode, etc.).
For this case, we'll probably eventually want to have something like: bcftools.nf (for BCFtools processes), manta.nf (for Manta processes), delly.nf (for DELLY processes), workflow-manta.nf (defines just the workflow for Manta using processes from manta.nf, bcftools.nf, etc. as needed), workflow-delly.nf (workflow for DELLY using processes from delly.nf, bcftools.nf, etc. as needed). No need to change it in this PR though, it can be done with the separation of the tools in future development

@tyamaguchi-ucla tyamaguchi-ucla added the enhancement New feature or request label Feb 22, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants