Merge pull request #86 from LabKey/fb_merge_discvr-20.11

Merge discvr-20.11 to develop

Author: bbimber

.github/workflows/sync-repos.yml

@@ -29,4 +29,4 @@ jobs:
           source_repo: "labkey/DiscvrLabKeyModules"
           source_branch: "develop"
           destination_branch: "develop"
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.PAT }}

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://api.travis-ci.com/BimberLab/DiscvrLabKeyModules.svg)](https://travis-ci.com/BimberLab/DiscvrLabKeyModules)
+![Build DISCVR](https://github.com/BimberLab/DiscvrLabKeyModules/workflows/Build%20DISCVR/badge.svg)
 
 ## Overview
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/RCommandWrapper.java

@@ -17,7 +17,6 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.reports.ExternalScriptEngineDefinition;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java

@@ -72,13 +72,13 @@ public Provider()
                     ToolParameterDescriptor.create(OUTPUT_GENBANK, "Create Genbank Output", "If selected, this will output a genbank file summarizing amplicons and primers", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true),
-                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--insert-type"), "insertType", "Insert Type", "The type of insert to detect.", "ldk-simplecombo", new JSONObject(){{
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--insert-name"), "insertType", "Insert Type", "The type of insert to detect.", "ldk-simplecombo", new JSONObject(){{
                         put("storeValues", "PiggyBac;Lentivirus");
                         put("allowBlank", false);
                     }}, "PiggyBac"),
                     ToolParameterDescriptor.create(DESIGN_PRIMERS, "Design Primers", "If selected, Primer3 will be used to design primers to flank integration sites", "checkbox", new JSONObject(){{
-                        put("checked", true);
-                    }}, true),
+                        put("checked", false);
+                    }}, false),
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--reads-to-output"), "readsToOutput", "Reads To Output Per Site", "If this is non-zero, up to this many reads per integration site will be written to a FASTA file.  This can serve as a way to verify the actual junction border.", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, null),