FDA-HFP Division of Surveillance & Data Integration WDL Library

Collection of utility WDL modules from the FDA Human Foods Program (CFSAN) DSDI Signal Detection and Bioinformatics branch.

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Importing

Typically you will import the tasks defined here into your own WDL workflows:

import https://github.com/CFSAN-Biostatistics/wdl-modules/raw/main/nanopore.wdl" as nanopore

and then use them in workflows:

call nanopore.assemble { fastq:my_reads }

WDL runners will collect these files as imports; there's not a reason to clone the repository unless you'd like to develop and submit additional tasks to the libraries. If that's something you'd like to do, please see CONTRIBUTING.rst to get started.

Usage

$ make help