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Create WDL workflow for Genbank submission #793

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dpark01 opened this issue Feb 22, 2018 · 0 comments · Fixed by #800
Closed

Create WDL workflow for Genbank submission #793

dpark01 opened this issue Feb 22, 2018 · 0 comments · Fixed by #800
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@dpark01
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dpark01 commented Feb 22, 2018

Create a WDL workflow for ncbi.py prep_genbank_files (and the various prerequisite steps leading up to that) that can prepare an assembly for submission to Genbank. Pull assembly stats from WDL outputs (e.g. the outputs of the plot_coverage WDL task) instead of Snakemake outputs (e.g. pipes/rules/reports_only) for the submission metadata.

Workflow should be a single-sample workflow that takes an assembly (fasta), assembly metrics (see above), a reference genome (fasta), reference annotation (gb), and outputs an NCBI tbl file. Possibly an asn file too if the user provides an authors.sbt and other such prerequisites.

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