Subworkflow Standards

[edmundmiller]

A follow-up to #662.

1. We need to think about the paths, and how users will install.

This one I haven't made a choice on. Currently, all the subworkflows don't work because the file paths in them are, for example, ../../modules/nf-core/software/samtools/stats/main but that nf-core isn't in the path. The double nested directories aren't my favorite, but I think they keep it consistent between this repo and the pipelines, so we don't have to sed all the include paths when installing. We'd have to move all the modules, which we should wait to do a second PR for, so we can verify the testing works in this one because moving everything is going to invoke #391.

2. We need to come up with a standard meta.yml for subworkflows and if there's anything different.
3. Some way to track down all the nf-core subworkflows that are floating in the pipelines

[mashehu]

ad 3.) Do you mean something like this nf-core/website#834 ? Or more something from the nf-core/tools side?

[edmundmiller]

No I just meant like GitHub issues, project or milestone to track the progress and creation of them. I think in the future yes something that ingests the meta.ymls and displays it on the site would be nice.