4. Using the WDL pipelines

Rather than chaining together viral-ngs pipeline steps as series of tool commands called in isolation, it is possible to execute them as a complete automated pipeline, from processing raw sequencer output to creating files suitable for GenBank submission. This utilizes the Workflow Description Language, which is documented at: https://github.com/openwdl/wdl

This documentation is not yet complete

4.1. Executing WDL workflows locally with Cromwell

See example here: https://github.com/broadinstitute/viral-ngs/blob/master/travis/tests-cromwell.sh

4.2. Executing WDL workflows on Google Cloud Platform with Cromwell

This should help: https://github.com/broadinstitute/viral-ngs/blob/master/pipes/WDL/cromwell.gcid-viral-seq.conf

4.3. Executing WDL workflows on FireCloud

More info later

4.4. Executing WDL workflows on DNAnexus

This is the primary mode of execution for many of our collaborators and lab members. You can obtain the latest versions here: https://platform.dnanexus.com/projects/F8PQ6380xf5bK0Qk0YPjB17P/data/