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

genbank workflow no longer accepts author.sbt file #490

Closed
dpark01 opened this issue Sep 27, 2023 · 1 comment · Fixed by #492
Closed

genbank workflow no longer accepts author.sbt file #490

dpark01 opened this issue Sep 27, 2023 · 1 comment · Fixed by #492
Assignees

Comments

@dpark01
Copy link
Member

dpark01 commented Sep 27, 2023

The recommended flow for submitting viral genomes to Genbank involves the end user creating and using an author.sbt file. This is probably still the best approach for bespoke sequencing projects. However, our current genbank.wdl workflow no longer accepts these files as input.

Recommend adding optional inputs and branching logic to workflow to allow either route (author.sbt file or author list + jinja template).

@tomkinsc
Copy link
Member

I think the genbank.wdl workflow will accept a properly-formatted authors.sbt file via the author_sbt_j2_template input if a blank yaml file is provided for author_sbt_defaults_yaml. The former input is named to indicate it expects a jinja2 template, but if there aren't any jinja2 directives in the template then the template (or an authors.sbt file provided in its place) should be passed through unchanged. We should verify that's true.

We could change the variable name and/or help string to make this more clear and also make the yaml input optional— creating a blank yaml on the fly if necessary, or branching to a different code path as you mention.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
2 participants