diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java index d8768ab6c..ad0dc435e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java @@ -78,15 +78,18 @@ public class GATKArgumentCollection { /** * By default, GATK generates a run report that is uploaded to a cloud-based service. This report contains basic - * non-identifying statistics (which tool was used, whether the run was successful etc.) that help us for debugging - * and development. You can use this option to turn off reporting if your run environment is not connected to the - * internet or if your data is subject to stringent confidentiality clauses (e.g. clinical patient data). - * To do so you will need to request a key using the online request form on our website. + * statistics about the run (which tool was used, whether the run was successful etc.) that help us for debugging + * and development. Up to version 3.2-2 the run report contains a record of the username and hostname associated + * with the run, but it does **NOT** contain any information that could be used to identify patient data. + * Nevertheless, if your data is subject to stringent confidentiality clauses (no outside communication) or if your + * run environment is not connected to the internet, you can disable the reporting system by seeting this option to + * "NO_ET". You will also need to request a key using the online request form on our website (se FAQs). */ @Argument(fullName = "phone_home", shortName = "et", doc="Run reporting mode", required = false) public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.AWS; /** - * Please see the online documentation FAQs for more details on the key system and how to request a key. + * Please see the "phone_home" argument below and the online documentation FAQs for more details on the key system + * and how to request a key. */ @Argument(fullName = "gatk_key", shortName = "K", doc="GATK key file required to run with -et NO_ET", required = false) public File gatkKeyFile = null;