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/