Allow user to override cellranger chemistry

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/CellRangerWrapper.java

@@ -95,6 +95,9 @@ public Provider()
                         put("extensions", Arrays.asList("gtf"));
                         put("width", 400);
                         put("allowBlank", false);
+                    }}, null),
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--chemistry"), "chemistry", "Chemistry", "This is usually left blank, in which case cellranger will auto-detect. Example values are: SC3Pv1, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R2, or SC5P-R1", "textfield", new JSONObject(){{
+
                     }}, null)
             ), PageFlowUtil.set("sequenceanalysis/field/GenomeFileSelectorField.js"), "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", true, false, ALIGNMENT_MODE.MERGE_THEN_ALIGN);
         }