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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).
The text was updated successfully, but these errors were encountered:
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.
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).
The text was updated successfully, but these errors were encountered: