diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java
index e78430b3f9..99135ede6b 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java
@@ -130,9 +130,9 @@ private RestResponse<ObjectMap> installCatalog() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), InstallationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "secretKey",commandOptions.secretKey, true);
-            putNestedIfNotEmpty(beanParams, "password",commandOptions.password, true);
-            putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
+            putNestedIfNotEmpty(beanParams, "secretKey", commandOptions.secretKey, true);
+            putNestedIfNotEmpty(beanParams, "password", commandOptions.password, true);
+            putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);
 
             installationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -161,7 +161,7 @@ private RestResponse<ObjectMap> jwtCatalog() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), JWTParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "secretKey",commandOptions.secretKey, true);
+            putNestedIfNotEmpty(beanParams, "secretKey", commandOptions.secretKey, true);
 
             jWTParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -186,11 +186,11 @@ private RestResponse<User> createUsers() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), UserCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
-            putNestedIfNotEmpty(beanParams, "password",commandOptions.password, true);
-            putNestedIfNotEmpty(beanParams, "organization",commandOptions.organization, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);
+            putNestedIfNotEmpty(beanParams, "password", commandOptions.password, true);
+            putNestedIfNotEmpty(beanParams, "organization", commandOptions.organization, true);
 
             userCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -219,11 +219,11 @@ private RestResponse<User> importUsers() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), UserImportParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "authenticationOriginId",commandOptions.authenticationOriginId, true);
-            putNestedIfNotNull(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotNull(beanParams, "resourceType",commandOptions.resourceType, true);
-            putNestedIfNotEmpty(beanParams, "study",commandOptions.study, true);
-            putNestedIfNotEmpty(beanParams, "studyGroup",commandOptions.studyGroup, true);
+            putNestedIfNotEmpty(beanParams, "authenticationOriginId", commandOptions.authenticationOriginId, true);
+            putNestedIfNotNull(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotNull(beanParams, "resourceType", commandOptions.resourceType, true);
+            putNestedIfNotEmpty(beanParams, "study", commandOptions.study, true);
+            putNestedIfNotEmpty(beanParams, "studyGroup", commandOptions.studyGroup, true);
 
             userImportParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -287,12 +287,12 @@ private RestResponse<Group> syncUsers() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), GroupSyncParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "authenticationOriginId",commandOptions.authenticationOriginId, true);
-            putNestedIfNotEmpty(beanParams, "from",commandOptions.from, true);
-            putNestedIfNotEmpty(beanParams, "to",commandOptions.to, true);
-            putNestedIfNotEmpty(beanParams, "study",commandOptions.study, true);
-            putNestedIfNotNull(beanParams, "syncAll",commandOptions.syncAll, true);
-            putNestedIfNotNull(beanParams, "force",commandOptions.force, true);
+            putNestedIfNotEmpty(beanParams, "authenticationOriginId", commandOptions.authenticationOriginId, true);
+            putNestedIfNotEmpty(beanParams, "from", commandOptions.from, true);
+            putNestedIfNotEmpty(beanParams, "to", commandOptions.to, true);
+            putNestedIfNotEmpty(beanParams, "study", commandOptions.study, true);
+            putNestedIfNotNull(beanParams, "syncAll", commandOptions.syncAll, true);
+            putNestedIfNotNull(beanParams, "force", commandOptions.force, true);
 
             groupSyncParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -322,8 +322,8 @@ private RestResponse<Group> usersUpdateGroups() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), UserUpdateGroup.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "studyIds",commandOptions.studyIds, true);
-            putNestedIfNotNull(beanParams, "groupIds",commandOptions.groupIds, true);
+            putNestedIfNotNull(beanParams, "studyIds", commandOptions.studyIds, true);
+            putNestedIfNotNull(beanParams, "groupIds", commandOptions.groupIds, true);
 
             userUpdateGroup = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java
index ddc77f0009..566389f36b 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java
@@ -140,12 +140,12 @@ private RestResponse<Job> runBwa() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), BwaWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
-            putNestedIfNotEmpty(beanParams, "fastaFile",commandOptions.fastaFile, true);
-            putNestedIfNotEmpty(beanParams, "fastq1File",commandOptions.fastq1File, true);
-            putNestedIfNotEmpty(beanParams, "fastq2File",commandOptions.fastq2File, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "bwaParams",commandOptions.bwaParams, true);
+            putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
+            putNestedIfNotEmpty(beanParams, "fastaFile", commandOptions.fastaFile, true);
+            putNestedIfNotEmpty(beanParams, "fastq1File", commandOptions.fastq1File, true);
+            putNestedIfNotEmpty(beanParams, "fastq2File", commandOptions.fastq2File, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "bwaParams", commandOptions.bwaParams, true);
 
             bwaWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -184,9 +184,9 @@ private RestResponse<Job> runCoverageIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CoverageIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "bamFileId",commandOptions.bamFileId, true);
-            putNestedIfNotEmpty(beanParams, "baiFileId",commandOptions.baiFileId, true);
-            putNestedIfNotNull(beanParams, "windowSize",commandOptions.windowSize, true);
+            putNestedIfNotEmpty(beanParams, "bamFileId", commandOptions.bamFileId, true);
+            putNestedIfNotEmpty(beanParams, "baiFileId", commandOptions.baiFileId, true);
+            putNestedIfNotNull(beanParams, "windowSize", commandOptions.windowSize, true);
 
             coverageIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -225,9 +225,9 @@ private RestResponse<Job> coverageQcGeneCoverageStatsRun() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), AlignmentGeneCoverageStatsParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "bamFile",commandOptions.bamFile, true);
-            putNestedIfNotNull(beanParams, "genes",commandOptions.genes, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "bamFile", commandOptions.bamFile, true);
+            putNestedIfNotNull(beanParams, "genes", commandOptions.genes, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             alignmentGeneCoverageStatsParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -323,9 +323,9 @@ private RestResponse<Job> runDeeptools() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), DeeptoolsWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "deeptoolsParams",commandOptions.deeptoolsParams, true);
+            putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "deeptoolsParams", commandOptions.deeptoolsParams, true);
 
             deeptoolsWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -364,9 +364,9 @@ private RestResponse<Job> runFastqc() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FastqcWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "inputFile",commandOptions.inputFile, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "fastqcParams",commandOptions.fastqcParams, true);
+            putNestedIfNotEmpty(beanParams, "inputFile", commandOptions.inputFile, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "fastqcParams", commandOptions.fastqcParams, true);
 
             fastqcWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -405,8 +405,8 @@ private RestResponse<Job> runIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), AlignmentIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "fileId",commandOptions.fileId, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
+            putNestedIfNotEmpty(beanParams, "fileId", commandOptions.fileId, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
 
             alignmentIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -445,9 +445,9 @@ private RestResponse<Job> runPicard() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PicardWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "picardParams",commandOptions.picardParams, true);
+            putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "picardParams", commandOptions.picardParams, true);
 
             picardWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -486,10 +486,10 @@ private RestResponse<Job> runQc() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), AlignmentQcParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "bamFile",commandOptions.bamFile, true);
-            putNestedIfNotEmpty(beanParams, "skip",commandOptions.skip, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "bamFile", commandOptions.bamFile, true);
+            putNestedIfNotEmpty(beanParams, "skip", commandOptions.skip, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             alignmentQcParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -560,10 +560,10 @@ private RestResponse<Job> runSamtools() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SamtoolsWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
-            putNestedIfNotEmpty(beanParams, "inputFile",commandOptions.inputFile, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "samtoolsParams",commandOptions.samtoolsParams, true);
+            putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
+            putNestedIfNotEmpty(beanParams, "inputFile", commandOptions.inputFile, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "samtoolsParams", commandOptions.samtoolsParams, true);
 
             samtoolsWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
index 9fca23c656..5e3150d36a 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
@@ -238,8 +238,8 @@ private RestResponse<ClinicalAnalysisAclEntryList> updateAcl() throws Exception
                     .readValue(new java.io.File(commandOptions.jsonFile), ClinicalAnalysisAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysis",commandOptions.clinicalAnalysis, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysis", commandOptions.clinicalAnalysis, true);
 
             clinicalAnalysisAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -273,7 +273,7 @@ private RestResponse<Job> loadAnnotationSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TsvAnnotationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
 
             tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -305,7 +305,7 @@ private RestResponse<ObjectMap> updateClinicalConfiguration() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ClinicalAnalysisStudyConfiguration.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "interpretation.defaultFilter",commandOptions.interpretationDefaultFilter, true);
+            putNestedMapIfNotEmpty(beanParams, "interpretation.defaultFilter", commandOptions.interpretationDefaultFilter, true);
 
             clinicalAnalysisStudyConfiguration = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -341,48 +341,48 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ClinicalAnalysisCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "disorder.id",commandOptions.disorderId, true);
-            putNestedIfNotEmpty(beanParams, "proband.id",commandOptions.probandId, true);
-            putNestedIfNotEmpty(beanParams, "family.id",commandOptions.familyId, true);
-            putNestedIfNotNull(beanParams, "panelLocked",commandOptions.panelLocked, true);
-            putNestedIfNotEmpty(beanParams, "analyst.id",commandOptions.analystId, true);
-            putNestedIfNotEmpty(beanParams, "report.title",commandOptions.reportTitle, true);
-            putNestedIfNotEmpty(beanParams, "report.overview",commandOptions.reportOverview, true);
-            putNestedIfNotEmpty(beanParams, "report.logo",commandOptions.reportLogo, true);
-            putNestedIfNotEmpty(beanParams, "report.signedBy",commandOptions.reportSignedBy, true);
-            putNestedIfNotEmpty(beanParams, "report.signature",commandOptions.reportSignature, true);
-            putNestedIfNotEmpty(beanParams, "report.date",commandOptions.reportDate, true);
-            putNestedIfNotEmpty(beanParams, "request.id",commandOptions.requestId, true);
-            putNestedIfNotEmpty(beanParams, "request.justification",commandOptions.requestJustification, true);
-            putNestedIfNotEmpty(beanParams, "request.date",commandOptions.requestDate, true);
-            putNestedIfNotNull(beanParams, "request.attributes",commandOptions.requestAttributes, true);
-            putNestedIfNotEmpty(beanParams, "responsible.id",commandOptions.responsibleId, true);
-            putNestedIfNotEmpty(beanParams, "responsible.name",commandOptions.responsibleName, true);
-            putNestedIfNotEmpty(beanParams, "responsible.email",commandOptions.responsibleEmail, true);
-            putNestedIfNotEmpty(beanParams, "responsible.organization",commandOptions.responsibleOrganization, true);
-            putNestedIfNotEmpty(beanParams, "responsible.department",commandOptions.responsibleDepartment, true);
-            putNestedIfNotEmpty(beanParams, "responsible.address",commandOptions.responsibleAddress, true);
-            putNestedIfNotEmpty(beanParams, "responsible.city",commandOptions.responsibleCity, true);
-            putNestedIfNotEmpty(beanParams, "responsible.postcode",commandOptions.responsiblePostcode, true);
-            putNestedIfNotEmpty(beanParams, "interpretation.name",commandOptions.interpretationName, true);
-            putNestedIfNotEmpty(beanParams, "interpretation.description",commandOptions.interpretationDescription, true);
-            putNestedIfNotEmpty(beanParams, "interpretation.clinicalAnalysisId",commandOptions.interpretationClinicalAnalysisId, true);
-            putNestedIfNotEmpty(beanParams, "interpretation.creationDate",commandOptions.interpretationCreationDate, true);
-            putNestedIfNotEmpty(beanParams, "interpretation.modificationDate",commandOptions.interpretationModificationDate, true);
-            putNestedIfNotNull(beanParams, "interpretation.locked",commandOptions.interpretationLocked, true);
-            putNestedIfNotNull(beanParams, "interpretation.attributes",commandOptions.interpretationAttributes, true);
-            putNestedIfNotNull(beanParams, "qualityControl.summary",commandOptions.qualityControlSummary, true);
-            putNestedIfNotNull(beanParams, "qualityControl.comments",commandOptions.qualityControlComments, true);
-            putNestedIfNotNull(beanParams, "qualityControl.files",commandOptions.qualityControlFiles, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "dueDate",commandOptions.dueDate, true);
-            putNestedIfNotEmpty(beanParams, "priority.id",commandOptions.priorityId, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "disorder.id", commandOptions.disorderId, true);
+            putNestedIfNotEmpty(beanParams, "proband.id", commandOptions.probandId, true);
+            putNestedIfNotEmpty(beanParams, "family.id", commandOptions.familyId, true);
+            putNestedIfNotNull(beanParams, "panelLocked", commandOptions.panelLocked, true);
+            putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
+            putNestedIfNotEmpty(beanParams, "report.title", commandOptions.reportTitle, true);
+            putNestedIfNotEmpty(beanParams, "report.overview", commandOptions.reportOverview, true);
+            putNestedIfNotEmpty(beanParams, "report.logo", commandOptions.reportLogo, true);
+            putNestedIfNotEmpty(beanParams, "report.signedBy", commandOptions.reportSignedBy, true);
+            putNestedIfNotEmpty(beanParams, "report.signature", commandOptions.reportSignature, true);
+            putNestedIfNotEmpty(beanParams, "report.date", commandOptions.reportDate, true);
+            putNestedIfNotEmpty(beanParams, "request.id", commandOptions.requestId, true);
+            putNestedIfNotEmpty(beanParams, "request.justification", commandOptions.requestJustification, true);
+            putNestedIfNotEmpty(beanParams, "request.date", commandOptions.requestDate, true);
+            putNestedMapIfNotEmpty(beanParams, "request.attributes", commandOptions.requestAttributes, true);
+            putNestedIfNotEmpty(beanParams, "responsible.id", commandOptions.responsibleId, true);
+            putNestedIfNotEmpty(beanParams, "responsible.name", commandOptions.responsibleName, true);
+            putNestedIfNotEmpty(beanParams, "responsible.email", commandOptions.responsibleEmail, true);
+            putNestedIfNotEmpty(beanParams, "responsible.organization", commandOptions.responsibleOrganization, true);
+            putNestedIfNotEmpty(beanParams, "responsible.department", commandOptions.responsibleDepartment, true);
+            putNestedIfNotEmpty(beanParams, "responsible.address", commandOptions.responsibleAddress, true);
+            putNestedIfNotEmpty(beanParams, "responsible.city", commandOptions.responsibleCity, true);
+            putNestedIfNotEmpty(beanParams, "responsible.postcode", commandOptions.responsiblePostcode, true);
+            putNestedIfNotEmpty(beanParams, "interpretation.name", commandOptions.interpretationName, true);
+            putNestedIfNotEmpty(beanParams, "interpretation.description", commandOptions.interpretationDescription, true);
+            putNestedIfNotEmpty(beanParams, "interpretation.clinicalAnalysisId", commandOptions.interpretationClinicalAnalysisId, true);
+            putNestedIfNotEmpty(beanParams, "interpretation.creationDate", commandOptions.interpretationCreationDate, true);
+            putNestedIfNotEmpty(beanParams, "interpretation.modificationDate", commandOptions.interpretationModificationDate, true);
+            putNestedIfNotNull(beanParams, "interpretation.locked", commandOptions.interpretationLocked, true);
+            putNestedMapIfNotEmpty(beanParams, "interpretation.attributes", commandOptions.interpretationAttributes, true);
+            putNestedIfNotNull(beanParams, "qualityControl.summary", commandOptions.qualityControlSummary, true);
+            putNestedIfNotNull(beanParams, "qualityControl.comments", commandOptions.qualityControlComments, true);
+            putNestedIfNotNull(beanParams, "qualityControl.files", commandOptions.qualityControlFiles, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "dueDate", commandOptions.dueDate, true);
+            putNestedIfNotEmpty(beanParams, "priority.id", commandOptions.priorityId, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
 
             clinicalAnalysisCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -541,9 +541,9 @@ private RestResponse<Job> runInterpreterCancerTiering() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CancerTieringInterpretationAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysis",commandOptions.clinicalAnalysis, true);
-            putNestedIfNotNull(beanParams, "discardedVariants",commandOptions.discardedVariants, true);
-            putNestedIfNotNull(beanParams, "primary",commandOptions.primary, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysis", commandOptions.clinicalAnalysis, true);
+            putNestedIfNotNull(beanParams, "discardedVariants", commandOptions.discardedVariants, true);
+            putNestedIfNotNull(beanParams, "primary", commandOptions.primary, true);
 
             cancerTieringInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -582,7 +582,7 @@ private RestResponse<Job> runInterpreterExomiser() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ExomiserInterpretationAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysis",commandOptions.clinicalAnalysis, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysis", commandOptions.clinicalAnalysis, true);
 
             exomiserInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -621,10 +621,10 @@ private RestResponse<Job> runInterpreterTeam() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TeamInterpretationAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysis",commandOptions.clinicalAnalysis, true);
-            putNestedIfNotNull(beanParams, "panels",commandOptions.panels, true);
-            putNestedIfNotEmpty(beanParams, "familySegregation",commandOptions.familySegregation, true);
-            putNestedIfNotNull(beanParams, "primary",commandOptions.primary, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysis", commandOptions.clinicalAnalysis, true);
+            putNestedIfNotNull(beanParams, "panels", commandOptions.panels, true);
+            putNestedIfNotEmpty(beanParams, "familySegregation", commandOptions.familySegregation, true);
+            putNestedIfNotNull(beanParams, "primary", commandOptions.primary, true);
 
             teamInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -663,10 +663,10 @@ private RestResponse<Job> runInterpreterTiering() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TieringInterpretationAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysis",commandOptions.clinicalAnalysis, true);
-            putNestedIfNotNull(beanParams, "panels",commandOptions.panels, true);
-            putNestedIfNotNull(beanParams, "penetrance",commandOptions.penetrance, true);
-            putNestedIfNotNull(beanParams, "primary",commandOptions.primary, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysis", commandOptions.clinicalAnalysis, true);
+            putNestedIfNotNull(beanParams, "panels", commandOptions.panels, true);
+            putNestedIfNotNull(beanParams, "penetrance", commandOptions.penetrance, true);
+            putNestedIfNotNull(beanParams, "primary", commandOptions.primary, true);
 
             tieringInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -705,57 +705,57 @@ private RestResponse<Job> runInterpreterZetta() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ZettaInterpretationAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysis",commandOptions.clinicalAnalysis, true);
-            putNestedIfNotNull(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotEmpty(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "study",commandOptions.bodyStudy, true);
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotEmpty(beanParams, "filter",commandOptions.filter, true);
-            putNestedIfNotEmpty(beanParams, "qual",commandOptions.qual, true);
-            putNestedIfNotEmpty(beanParams, "fileData",commandOptions.fileData, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "sampleData",commandOptions.sampleData, true);
-            putNestedIfNotEmpty(beanParams, "sampleAnnotation",commandOptions.sampleAnnotation, true);
-            putNestedIfNotEmpty(beanParams, "sampleMetadata",commandOptions.sampleMetadata, true);
-            putNestedIfNotEmpty(beanParams, "cohort",commandOptions.cohort, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsRef",commandOptions.cohortStatsRef, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsAlt",commandOptions.cohortStatsAlt, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsMaf",commandOptions.cohortStatsMaf, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsMgf",commandOptions.cohortStatsMgf, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsPass",commandOptions.cohortStatsPass, true);
-            putNestedIfNotEmpty(beanParams, "score",commandOptions.score, true);
-            putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotEmpty(beanParams, "familyDisorder",commandOptions.familyDisorder, true);
-            putNestedIfNotEmpty(beanParams, "familySegregation",commandOptions.familySegregation, true);
-            putNestedIfNotEmpty(beanParams, "familyMembers",commandOptions.familyMembers, true);
-            putNestedIfNotEmpty(beanParams, "familyProband",commandOptions.familyProband, true);
-            putNestedIfNotEmpty(beanParams, "gene",commandOptions.gene, true);
-            putNestedIfNotEmpty(beanParams, "ct",commandOptions.ct, true);
-            putNestedIfNotEmpty(beanParams, "xref",commandOptions.xref, true);
-            putNestedIfNotEmpty(beanParams, "biotype",commandOptions.biotype, true);
-            putNestedIfNotEmpty(beanParams, "proteinSubstitution",commandOptions.proteinSubstitution, true);
-            putNestedIfNotEmpty(beanParams, "conservation",commandOptions.conservation, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyAlt",commandOptions.populationFrequencyAlt, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyRef",commandOptions.populationFrequencyRef, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyMaf",commandOptions.populationFrequencyMaf, true);
-            putNestedIfNotEmpty(beanParams, "transcriptFlag",commandOptions.transcriptFlag, true);
-            putNestedIfNotEmpty(beanParams, "geneTraitId",commandOptions.geneTraitId, true);
-            putNestedIfNotEmpty(beanParams, "go",commandOptions.go, true);
-            putNestedIfNotEmpty(beanParams, "expression",commandOptions.expression, true);
-            putNestedIfNotEmpty(beanParams, "proteinKeyword",commandOptions.proteinKeyword, true);
-            putNestedIfNotEmpty(beanParams, "drug",commandOptions.drug, true);
-            putNestedIfNotEmpty(beanParams, "functionalScore",commandOptions.functionalScore, true);
-            putNestedIfNotEmpty(beanParams, "clinical",commandOptions.clinical, true);
-            putNestedIfNotEmpty(beanParams, "clinicalSignificance",commandOptions.clinicalSignificance, true);
-            putNestedIfNotNull(beanParams, "clinicalConfirmedStatus",commandOptions.clinicalConfirmedStatus, true);
-            putNestedIfNotEmpty(beanParams, "customAnnotation",commandOptions.customAnnotation, true);
-            putNestedIfNotEmpty(beanParams, "panel",commandOptions.panel, true);
-            putNestedIfNotEmpty(beanParams, "panelModeOfInheritance",commandOptions.panelModeOfInheritance, true);
-            putNestedIfNotEmpty(beanParams, "panelConfidence",commandOptions.panelConfidence, true);
-            putNestedIfNotEmpty(beanParams, "panelRoleInCancer",commandOptions.panelRoleInCancer, true);
-            putNestedIfNotEmpty(beanParams, "trait",commandOptions.trait, true);
-            putNestedIfNotNull(beanParams, "primary",commandOptions.primary, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysis", commandOptions.clinicalAnalysis, true);
+            putNestedIfNotNull(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotEmpty(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "study", commandOptions.bodyStudy, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotEmpty(beanParams, "filter", commandOptions.filter, true);
+            putNestedIfNotEmpty(beanParams, "qual", commandOptions.qual, true);
+            putNestedIfNotEmpty(beanParams, "fileData", commandOptions.fileData, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "sampleData", commandOptions.sampleData, true);
+            putNestedIfNotEmpty(beanParams, "sampleAnnotation", commandOptions.sampleAnnotation, true);
+            putNestedIfNotEmpty(beanParams, "sampleMetadata", commandOptions.sampleMetadata, true);
+            putNestedIfNotEmpty(beanParams, "cohort", commandOptions.cohort, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsRef", commandOptions.cohortStatsRef, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsAlt", commandOptions.cohortStatsAlt, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsMaf", commandOptions.cohortStatsMaf, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsMgf", commandOptions.cohortStatsMgf, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsPass", commandOptions.cohortStatsPass, true);
+            putNestedIfNotEmpty(beanParams, "score", commandOptions.score, true);
+            putNestedIfNotEmpty(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotEmpty(beanParams, "familyDisorder", commandOptions.familyDisorder, true);
+            putNestedIfNotEmpty(beanParams, "familySegregation", commandOptions.familySegregation, true);
+            putNestedIfNotEmpty(beanParams, "familyMembers", commandOptions.familyMembers, true);
+            putNestedIfNotEmpty(beanParams, "familyProband", commandOptions.familyProband, true);
+            putNestedIfNotEmpty(beanParams, "gene", commandOptions.gene, true);
+            putNestedIfNotEmpty(beanParams, "ct", commandOptions.ct, true);
+            putNestedIfNotEmpty(beanParams, "xref", commandOptions.xref, true);
+            putNestedIfNotEmpty(beanParams, "biotype", commandOptions.biotype, true);
+            putNestedIfNotEmpty(beanParams, "proteinSubstitution", commandOptions.proteinSubstitution, true);
+            putNestedIfNotEmpty(beanParams, "conservation", commandOptions.conservation, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyAlt", commandOptions.populationFrequencyAlt, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyRef", commandOptions.populationFrequencyRef, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyMaf", commandOptions.populationFrequencyMaf, true);
+            putNestedIfNotEmpty(beanParams, "transcriptFlag", commandOptions.transcriptFlag, true);
+            putNestedIfNotEmpty(beanParams, "geneTraitId", commandOptions.geneTraitId, true);
+            putNestedIfNotEmpty(beanParams, "go", commandOptions.go, true);
+            putNestedIfNotEmpty(beanParams, "expression", commandOptions.expression, true);
+            putNestedIfNotEmpty(beanParams, "proteinKeyword", commandOptions.proteinKeyword, true);
+            putNestedIfNotEmpty(beanParams, "drug", commandOptions.drug, true);
+            putNestedIfNotEmpty(beanParams, "functionalScore", commandOptions.functionalScore, true);
+            putNestedIfNotEmpty(beanParams, "clinical", commandOptions.clinical, true);
+            putNestedIfNotEmpty(beanParams, "clinicalSignificance", commandOptions.clinicalSignificance, true);
+            putNestedIfNotNull(beanParams, "clinicalConfirmedStatus", commandOptions.clinicalConfirmedStatus, true);
+            putNestedIfNotEmpty(beanParams, "customAnnotation", commandOptions.customAnnotation, true);
+            putNestedIfNotEmpty(beanParams, "panel", commandOptions.panel, true);
+            putNestedIfNotEmpty(beanParams, "panelModeOfInheritance", commandOptions.panelModeOfInheritance, true);
+            putNestedIfNotEmpty(beanParams, "panelConfidence", commandOptions.panelConfidence, true);
+            putNestedIfNotEmpty(beanParams, "panelRoleInCancer", commandOptions.panelRoleInCancer, true);
+            putNestedIfNotEmpty(beanParams, "trait", commandOptions.trait, true);
+            putNestedIfNotNull(beanParams, "primary", commandOptions.primary, true);
 
             zettaInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -794,7 +794,7 @@ private RestResponse<Job> load() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ClinicalAnalysisLoadParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
 
             clinicalAnalysisLoadParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -949,7 +949,7 @@ private RestResponse<Job> runRgaIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), RgaAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
 
             rgaAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1293,43 +1293,43 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ClinicalAnalysisUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "disorder.id",commandOptions.disorderId, true);
-            putNestedIfNotNull(beanParams, "panelLocked",commandOptions.panelLocked, true);
-            putNestedIfNotEmpty(beanParams, "proband.id",commandOptions.probandId, true);
-            putNestedIfNotEmpty(beanParams, "family.id",commandOptions.familyId, true);
-            putNestedIfNotNull(beanParams, "locked",commandOptions.locked, true);
-            putNestedIfNotEmpty(beanParams, "analyst.id",commandOptions.analystId, true);
-            putNestedIfNotEmpty(beanParams, "report.title",commandOptions.reportTitle, true);
-            putNestedIfNotEmpty(beanParams, "report.overview",commandOptions.reportOverview, true);
-            putNestedIfNotEmpty(beanParams, "report.logo",commandOptions.reportLogo, true);
-            putNestedIfNotEmpty(beanParams, "report.signedBy",commandOptions.reportSignedBy, true);
-            putNestedIfNotEmpty(beanParams, "report.signature",commandOptions.reportSignature, true);
-            putNestedIfNotEmpty(beanParams, "report.date",commandOptions.reportDate, true);
-            putNestedIfNotEmpty(beanParams, "request.id",commandOptions.requestId, true);
-            putNestedIfNotEmpty(beanParams, "request.justification",commandOptions.requestJustification, true);
-            putNestedIfNotEmpty(beanParams, "request.date",commandOptions.requestDate, true);
-            putNestedIfNotNull(beanParams, "request.attributes",commandOptions.requestAttributes, true);
-            putNestedIfNotEmpty(beanParams, "responsible.id",commandOptions.responsibleId, true);
-            putNestedIfNotEmpty(beanParams, "responsible.name",commandOptions.responsibleName, true);
-            putNestedIfNotEmpty(beanParams, "responsible.email",commandOptions.responsibleEmail, true);
-            putNestedIfNotEmpty(beanParams, "responsible.organization",commandOptions.responsibleOrganization, true);
-            putNestedIfNotEmpty(beanParams, "responsible.department",commandOptions.responsibleDepartment, true);
-            putNestedIfNotEmpty(beanParams, "responsible.address",commandOptions.responsibleAddress, true);
-            putNestedIfNotEmpty(beanParams, "responsible.city",commandOptions.responsibleCity, true);
-            putNestedIfNotEmpty(beanParams, "responsible.postcode",commandOptions.responsiblePostcode, true);
-            putNestedIfNotNull(beanParams, "qualityControl.summary",commandOptions.qualityControlSummary, true);
-            putNestedIfNotNull(beanParams, "qualityControl.comments",commandOptions.qualityControlComments, true);
-            putNestedIfNotNull(beanParams, "qualityControl.files",commandOptions.qualityControlFiles, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "dueDate",commandOptions.dueDate, true);
-            putNestedIfNotEmpty(beanParams, "priority.id",commandOptions.priorityId, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotNull(beanParams, "panelLock",commandOptions.panelLock, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "disorder.id", commandOptions.disorderId, true);
+            putNestedIfNotNull(beanParams, "panelLocked", commandOptions.panelLocked, true);
+            putNestedIfNotEmpty(beanParams, "proband.id", commandOptions.probandId, true);
+            putNestedIfNotEmpty(beanParams, "family.id", commandOptions.familyId, true);
+            putNestedIfNotNull(beanParams, "locked", commandOptions.locked, true);
+            putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
+            putNestedIfNotEmpty(beanParams, "report.title", commandOptions.reportTitle, true);
+            putNestedIfNotEmpty(beanParams, "report.overview", commandOptions.reportOverview, true);
+            putNestedIfNotEmpty(beanParams, "report.logo", commandOptions.reportLogo, true);
+            putNestedIfNotEmpty(beanParams, "report.signedBy", commandOptions.reportSignedBy, true);
+            putNestedIfNotEmpty(beanParams, "report.signature", commandOptions.reportSignature, true);
+            putNestedIfNotEmpty(beanParams, "report.date", commandOptions.reportDate, true);
+            putNestedIfNotEmpty(beanParams, "request.id", commandOptions.requestId, true);
+            putNestedIfNotEmpty(beanParams, "request.justification", commandOptions.requestJustification, true);
+            putNestedIfNotEmpty(beanParams, "request.date", commandOptions.requestDate, true);
+            putNestedMapIfNotEmpty(beanParams, "request.attributes", commandOptions.requestAttributes, true);
+            putNestedIfNotEmpty(beanParams, "responsible.id", commandOptions.responsibleId, true);
+            putNestedIfNotEmpty(beanParams, "responsible.name", commandOptions.responsibleName, true);
+            putNestedIfNotEmpty(beanParams, "responsible.email", commandOptions.responsibleEmail, true);
+            putNestedIfNotEmpty(beanParams, "responsible.organization", commandOptions.responsibleOrganization, true);
+            putNestedIfNotEmpty(beanParams, "responsible.department", commandOptions.responsibleDepartment, true);
+            putNestedIfNotEmpty(beanParams, "responsible.address", commandOptions.responsibleAddress, true);
+            putNestedIfNotEmpty(beanParams, "responsible.city", commandOptions.responsibleCity, true);
+            putNestedIfNotEmpty(beanParams, "responsible.postcode", commandOptions.responsiblePostcode, true);
+            putNestedIfNotNull(beanParams, "qualityControl.summary", commandOptions.qualityControlSummary, true);
+            putNestedIfNotNull(beanParams, "qualityControl.comments", commandOptions.qualityControlComments, true);
+            putNestedIfNotNull(beanParams, "qualityControl.files", commandOptions.qualityControlFiles, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "dueDate", commandOptions.dueDate, true);
+            putNestedIfNotEmpty(beanParams, "priority.id", commandOptions.priorityId, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);
 
             clinicalAnalysisUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1410,18 +1410,18 @@ private RestResponse<Interpretation> createInterpretation() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), InterpretationCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysisId",commandOptions.clinicalAnalysisId, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "analyst.id",commandOptions.analystId, true);
-            putNestedIfNotEmpty(beanParams, "method.name",commandOptions.methodName, true);
-            putNestedIfNotEmpty(beanParams, "method.version",commandOptions.methodVersion, true);
-            putNestedIfNotEmpty(beanParams, "method.commit",commandOptions.methodCommit, true);
-            putNestedIfNotNull(beanParams, "locked",commandOptions.locked, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysisId", commandOptions.clinicalAnalysisId, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
+            putNestedIfNotEmpty(beanParams, "method.name", commandOptions.methodName, true);
+            putNestedIfNotEmpty(beanParams, "method.version", commandOptions.methodVersion, true);
+            putNestedIfNotEmpty(beanParams, "method.commit", commandOptions.methodCommit, true);
+            putNestedIfNotNull(beanParams, "locked", commandOptions.locked, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             interpretationCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1500,17 +1500,17 @@ private RestResponse<Interpretation> updateInterpretation() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), InterpretationUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "analyst.id",commandOptions.analystId, true);
-            putNestedIfNotEmpty(beanParams, "method.name",commandOptions.methodName, true);
-            putNestedIfNotEmpty(beanParams, "method.version",commandOptions.methodVersion, true);
-            putNestedIfNotEmpty(beanParams, "method.commit",commandOptions.methodCommit, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotNull(beanParams, "locked",commandOptions.locked, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
+            putNestedIfNotEmpty(beanParams, "method.name", commandOptions.methodName, true);
+            putNestedIfNotEmpty(beanParams, "method.version", commandOptions.methodVersion, true);
+            putNestedIfNotEmpty(beanParams, "method.commit", commandOptions.methodCommit, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotNull(beanParams, "locked", commandOptions.locked, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             interpretationUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1546,15 +1546,15 @@ private RestResponse<ClinicalReport> updateReport() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ClinicalReport.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "title",commandOptions.title, true);
-            putNestedIfNotEmpty(beanParams, "overview",commandOptions.overview, true);
-            putNestedIfNotEmpty(beanParams, "discussion.author",commandOptions.discussionAuthor, true);
-            putNestedIfNotEmpty(beanParams, "discussion.date",commandOptions.discussionDate, true);
-            putNestedIfNotEmpty(beanParams, "discussion.text",commandOptions.discussionText, true);
-            putNestedIfNotEmpty(beanParams, "logo",commandOptions.logo, true);
-            putNestedIfNotEmpty(beanParams, "signedBy",commandOptions.signedBy, true);
-            putNestedIfNotEmpty(beanParams, "signature",commandOptions.signature, true);
-            putNestedIfNotEmpty(beanParams, "date",commandOptions.date, true);
+            putNestedIfNotEmpty(beanParams, "title", commandOptions.title, true);
+            putNestedIfNotEmpty(beanParams, "overview", commandOptions.overview, true);
+            putNestedIfNotEmpty(beanParams, "discussion.author", commandOptions.discussionAuthor, true);
+            putNestedIfNotEmpty(beanParams, "discussion.date", commandOptions.discussionDate, true);
+            putNestedIfNotEmpty(beanParams, "discussion.text", commandOptions.discussionText, true);
+            putNestedIfNotEmpty(beanParams, "logo", commandOptions.logo, true);
+            putNestedIfNotEmpty(beanParams, "signedBy", commandOptions.signedBy, true);
+            putNestedIfNotEmpty(beanParams, "signature", commandOptions.signature, true);
+            putNestedIfNotEmpty(beanParams, "date", commandOptions.date, true);
 
             clinicalReport = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java
index 3427a69163..316985784d 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java
@@ -318,10 +318,10 @@ private RestResponse<String> runCircos() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CircosAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "title",commandOptions.title, true);
-            putNestedIfNotEmpty(beanParams, "density",commandOptions.density, true);
-            putNestedIfNotNull(beanParams, "query",commandOptions.query, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "title", commandOptions.title, true);
+            putNestedIfNotEmpty(beanParams, "density", commandOptions.density, true);
+            putNestedMapIfNotEmpty(beanParams, "query", commandOptions.query, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             circosAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -389,11 +389,11 @@ private RestResponse<Job> runCohortStats() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CohortVariantStatsAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "cohort",commandOptions.cohort, true);
-            putNestedIfNotNull(beanParams, "samples",commandOptions.samples, true);
-            putNestedIfNotNull(beanParams, "index",commandOptions.index, true);
-            putNestedIfNotEmpty(beanParams, "sampleAnnotation",commandOptions.sampleAnnotation, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "cohort", commandOptions.cohort, true);
+            putNestedIfNotNull(beanParams, "samples", commandOptions.samples, true);
+            putNestedIfNotNull(beanParams, "index", commandOptions.index, true);
+            putNestedIfNotEmpty(beanParams, "sampleAnnotation", commandOptions.sampleAnnotation, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             cohortVariantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -432,9 +432,9 @@ private RestResponse<Job> runExomiser() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ExomiserWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "clinicalAnalysisType",commandOptions.clinicalAnalysisType, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "clinicalAnalysisType", commandOptions.clinicalAnalysisType, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             exomiserWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -476,93 +476,93 @@ private RestResponse<Job> runExport() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantExportParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotEmpty(beanParams, "gene",commandOptions.gene, true);
-            putNestedIfNotEmpty(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "panel",commandOptions.panel, true);
-            putNestedIfNotEmpty(beanParams, "panelModeOfInheritance",commandOptions.panelModeOfInheritance, true);
-            putNestedIfNotEmpty(beanParams, "panelConfidence",commandOptions.panelConfidence, true);
-            putNestedIfNotEmpty(beanParams, "panelRoleInCancer",commandOptions.panelRoleInCancer, true);
-            putNestedIfNotNull(beanParams, "panelIntersection",commandOptions.panelIntersection, true);
-            putNestedIfNotEmpty(beanParams, "panelFeatureType",commandOptions.panelFeatureType, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsRef",commandOptions.cohortStatsRef, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsAlt",commandOptions.cohortStatsAlt, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsMaf",commandOptions.cohortStatsMaf, true);
-            putNestedIfNotEmpty(beanParams, "ct",commandOptions.ct, true);
-            putNestedIfNotEmpty(beanParams, "xref",commandOptions.xref, true);
-            putNestedIfNotEmpty(beanParams, "biotype",commandOptions.biotype, true);
-            putNestedIfNotEmpty(beanParams, "proteinSubstitution",commandOptions.proteinSubstitution, true);
-            putNestedIfNotEmpty(beanParams, "conservation",commandOptions.conservation, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyMaf",commandOptions.populationFrequencyMaf, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyAlt",commandOptions.populationFrequencyAlt, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyRef",commandOptions.populationFrequencyRef, true);
-            putNestedIfNotEmpty(beanParams, "transcriptFlag",commandOptions.transcriptFlag, true);
-            putNestedIfNotEmpty(beanParams, "functionalScore",commandOptions.functionalScore, true);
-            putNestedIfNotEmpty(beanParams, "clinical",commandOptions.clinical, true);
-            putNestedIfNotEmpty(beanParams, "clinicalSignificance",commandOptions.clinicalSignificance, true);
-            putNestedIfNotNull(beanParams, "clinicalConfirmedStatus",commandOptions.clinicalConfirmedStatus, true);
-            putNestedIfNotEmpty(beanParams, "project",commandOptions.bodyProject, true);
-            putNestedIfNotEmpty(beanParams, "study",commandOptions.bodyStudy, true);
-            putNestedIfNotEmpty(beanParams, "savedFilter",commandOptions.savedFilter, true);
-            putNestedIfNotEmpty(beanParams, "chromosome",commandOptions.chromosome, true);
-            putNestedIfNotEmpty(beanParams, "reference",commandOptions.reference, true);
-            putNestedIfNotEmpty(beanParams, "alternate",commandOptions.alternate, true);
-            putNestedIfNotEmpty(beanParams, "release",commandOptions.release, true);
-            putNestedIfNotEmpty(beanParams, "includeStudy",commandOptions.includeStudy, true);
-            putNestedIfNotEmpty(beanParams, "includeSample",commandOptions.includeSample, true);
-            putNestedIfNotEmpty(beanParams, "includeFile",commandOptions.includeFile, true);
-            putNestedIfNotEmpty(beanParams, "includeSampleData",commandOptions.includeSampleData, true);
-            putNestedIfNotNull(beanParams, "includeSampleId",commandOptions.includeSampleId, true);
-            putNestedIfNotNull(beanParams, "includeGenotype",commandOptions.includeGenotype, true);
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotEmpty(beanParams, "qual",commandOptions.qual, true);
-            putNestedIfNotEmpty(beanParams, "filter",commandOptions.filter, true);
-            putNestedIfNotEmpty(beanParams, "fileData",commandOptions.fileData, true);
-            putNestedIfNotEmpty(beanParams, "genotype",commandOptions.genotype, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "sampleLimit",commandOptions.sampleLimit, true);
-            putNestedIfNotNull(beanParams, "sampleSkip",commandOptions.sampleSkip, true);
-            putNestedIfNotEmpty(beanParams, "sampleData",commandOptions.sampleData, true);
-            putNestedIfNotEmpty(beanParams, "sampleAnnotation",commandOptions.sampleAnnotation, true);
-            putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotEmpty(beanParams, "familyMembers",commandOptions.familyMembers, true);
-            putNestedIfNotEmpty(beanParams, "familyDisorder",commandOptions.familyDisorder, true);
-            putNestedIfNotEmpty(beanParams, "familyProband",commandOptions.familyProband, true);
-            putNestedIfNotEmpty(beanParams, "familySegregation",commandOptions.familySegregation, true);
-            putNestedIfNotEmpty(beanParams, "cohort",commandOptions.cohort, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsPass",commandOptions.cohortStatsPass, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsMgf",commandOptions.cohortStatsMgf, true);
-            putNestedIfNotEmpty(beanParams, "missingAlleles",commandOptions.missingAlleles, true);
-            putNestedIfNotEmpty(beanParams, "missingGenotypes",commandOptions.missingGenotypes, true);
-            putNestedIfNotNull(beanParams, "annotationExists",commandOptions.annotationExists, true);
-            putNestedIfNotEmpty(beanParams, "score",commandOptions.score, true);
-            putNestedIfNotEmpty(beanParams, "polyphen",commandOptions.polyphen, true);
-            putNestedIfNotEmpty(beanParams, "sift",commandOptions.sift, true);
-            putNestedIfNotEmpty(beanParams, "geneRoleInCancer",commandOptions.geneRoleInCancer, true);
-            putNestedIfNotEmpty(beanParams, "geneTraitId",commandOptions.geneTraitId, true);
-            putNestedIfNotEmpty(beanParams, "geneTraitName",commandOptions.geneTraitName, true);
-            putNestedIfNotEmpty(beanParams, "trait",commandOptions.trait, true);
-            putNestedIfNotEmpty(beanParams, "cosmic",commandOptions.cosmic, true);
-            putNestedIfNotEmpty(beanParams, "clinvar",commandOptions.clinvar, true);
-            putNestedIfNotEmpty(beanParams, "hpo",commandOptions.hpo, true);
-            putNestedIfNotEmpty(beanParams, "go",commandOptions.go, true);
-            putNestedIfNotEmpty(beanParams, "expression",commandOptions.expression, true);
-            putNestedIfNotEmpty(beanParams, "proteinKeyword",commandOptions.proteinKeyword, true);
-            putNestedIfNotEmpty(beanParams, "drug",commandOptions.drug, true);
-            putNestedIfNotEmpty(beanParams, "customAnnotation",commandOptions.customAnnotation, true);
-            putNestedIfNotEmpty(beanParams, "unknownGenotype",commandOptions.unknownGenotype, true);
-            putNestedIfNotNull(beanParams, "sampleMetadata",commandOptions.sampleMetadata, true);
-            putNestedIfNotNull(beanParams, "sort",commandOptions.sort, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotEmpty(beanParams, "outputFileName",commandOptions.outputFileName, true);
-            putNestedIfNotEmpty(beanParams, "outputFileFormat",commandOptions.outputFileFormat, true);
-            putNestedIfNotEmpty(beanParams, "variantsFile",commandOptions.variantsFile, true);
-            putNestedIfNotEmpty(beanParams, "include",commandOptions.bodyInclude, true);
-            putNestedIfNotEmpty(beanParams, "exclude",commandOptions.bodyExclude, true);
-            putNestedIfNotNull(beanParams, "limit",commandOptions.limit, true);
-            putNestedIfNotNull(beanParams, "skip",commandOptions.skip, true);
-            putNestedIfNotNull(beanParams, "summary",commandOptions.summary, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotEmpty(beanParams, "gene", commandOptions.gene, true);
+            putNestedIfNotEmpty(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "panel", commandOptions.panel, true);
+            putNestedIfNotEmpty(beanParams, "panelModeOfInheritance", commandOptions.panelModeOfInheritance, true);
+            putNestedIfNotEmpty(beanParams, "panelConfidence", commandOptions.panelConfidence, true);
+            putNestedIfNotEmpty(beanParams, "panelRoleInCancer", commandOptions.panelRoleInCancer, true);
+            putNestedIfNotNull(beanParams, "panelIntersection", commandOptions.panelIntersection, true);
+            putNestedIfNotEmpty(beanParams, "panelFeatureType", commandOptions.panelFeatureType, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsRef", commandOptions.cohortStatsRef, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsAlt", commandOptions.cohortStatsAlt, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsMaf", commandOptions.cohortStatsMaf, true);
+            putNestedIfNotEmpty(beanParams, "ct", commandOptions.ct, true);
+            putNestedIfNotEmpty(beanParams, "xref", commandOptions.xref, true);
+            putNestedIfNotEmpty(beanParams, "biotype", commandOptions.biotype, true);
+            putNestedIfNotEmpty(beanParams, "proteinSubstitution", commandOptions.proteinSubstitution, true);
+            putNestedIfNotEmpty(beanParams, "conservation", commandOptions.conservation, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyMaf", commandOptions.populationFrequencyMaf, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyAlt", commandOptions.populationFrequencyAlt, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyRef", commandOptions.populationFrequencyRef, true);
+            putNestedIfNotEmpty(beanParams, "transcriptFlag", commandOptions.transcriptFlag, true);
+            putNestedIfNotEmpty(beanParams, "functionalScore", commandOptions.functionalScore, true);
+            putNestedIfNotEmpty(beanParams, "clinical", commandOptions.clinical, true);
+            putNestedIfNotEmpty(beanParams, "clinicalSignificance", commandOptions.clinicalSignificance, true);
+            putNestedIfNotNull(beanParams, "clinicalConfirmedStatus", commandOptions.clinicalConfirmedStatus, true);
+            putNestedIfNotEmpty(beanParams, "project", commandOptions.bodyProject, true);
+            putNestedIfNotEmpty(beanParams, "study", commandOptions.bodyStudy, true);
+            putNestedIfNotEmpty(beanParams, "savedFilter", commandOptions.savedFilter, true);
+            putNestedIfNotEmpty(beanParams, "chromosome", commandOptions.chromosome, true);
+            putNestedIfNotEmpty(beanParams, "reference", commandOptions.reference, true);
+            putNestedIfNotEmpty(beanParams, "alternate", commandOptions.alternate, true);
+            putNestedIfNotEmpty(beanParams, "release", commandOptions.release, true);
+            putNestedIfNotEmpty(beanParams, "includeStudy", commandOptions.includeStudy, true);
+            putNestedIfNotEmpty(beanParams, "includeSample", commandOptions.includeSample, true);
+            putNestedIfNotEmpty(beanParams, "includeFile", commandOptions.includeFile, true);
+            putNestedIfNotEmpty(beanParams, "includeSampleData", commandOptions.includeSampleData, true);
+            putNestedIfNotNull(beanParams, "includeSampleId", commandOptions.includeSampleId, true);
+            putNestedIfNotNull(beanParams, "includeGenotype", commandOptions.includeGenotype, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotEmpty(beanParams, "qual", commandOptions.qual, true);
+            putNestedIfNotEmpty(beanParams, "filter", commandOptions.filter, true);
+            putNestedIfNotEmpty(beanParams, "fileData", commandOptions.fileData, true);
+            putNestedIfNotEmpty(beanParams, "genotype", commandOptions.genotype, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "sampleLimit", commandOptions.sampleLimit, true);
+            putNestedIfNotNull(beanParams, "sampleSkip", commandOptions.sampleSkip, true);
+            putNestedIfNotEmpty(beanParams, "sampleData", commandOptions.sampleData, true);
+            putNestedIfNotEmpty(beanParams, "sampleAnnotation", commandOptions.sampleAnnotation, true);
+            putNestedIfNotEmpty(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotEmpty(beanParams, "familyMembers", commandOptions.familyMembers, true);
+            putNestedIfNotEmpty(beanParams, "familyDisorder", commandOptions.familyDisorder, true);
+            putNestedIfNotEmpty(beanParams, "familyProband", commandOptions.familyProband, true);
+            putNestedIfNotEmpty(beanParams, "familySegregation", commandOptions.familySegregation, true);
+            putNestedIfNotEmpty(beanParams, "cohort", commandOptions.cohort, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsPass", commandOptions.cohortStatsPass, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsMgf", commandOptions.cohortStatsMgf, true);
+            putNestedIfNotEmpty(beanParams, "missingAlleles", commandOptions.missingAlleles, true);
+            putNestedIfNotEmpty(beanParams, "missingGenotypes", commandOptions.missingGenotypes, true);
+            putNestedIfNotNull(beanParams, "annotationExists", commandOptions.annotationExists, true);
+            putNestedIfNotEmpty(beanParams, "score", commandOptions.score, true);
+            putNestedIfNotEmpty(beanParams, "polyphen", commandOptions.polyphen, true);
+            putNestedIfNotEmpty(beanParams, "sift", commandOptions.sift, true);
+            putNestedIfNotEmpty(beanParams, "geneRoleInCancer", commandOptions.geneRoleInCancer, true);
+            putNestedIfNotEmpty(beanParams, "geneTraitId", commandOptions.geneTraitId, true);
+            putNestedIfNotEmpty(beanParams, "geneTraitName", commandOptions.geneTraitName, true);
+            putNestedIfNotEmpty(beanParams, "trait", commandOptions.trait, true);
+            putNestedIfNotEmpty(beanParams, "cosmic", commandOptions.cosmic, true);
+            putNestedIfNotEmpty(beanParams, "clinvar", commandOptions.clinvar, true);
+            putNestedIfNotEmpty(beanParams, "hpo", commandOptions.hpo, true);
+            putNestedIfNotEmpty(beanParams, "go", commandOptions.go, true);
+            putNestedIfNotEmpty(beanParams, "expression", commandOptions.expression, true);
+            putNestedIfNotEmpty(beanParams, "proteinKeyword", commandOptions.proteinKeyword, true);
+            putNestedIfNotEmpty(beanParams, "drug", commandOptions.drug, true);
+            putNestedIfNotEmpty(beanParams, "customAnnotation", commandOptions.customAnnotation, true);
+            putNestedIfNotEmpty(beanParams, "unknownGenotype", commandOptions.unknownGenotype, true);
+            putNestedIfNotNull(beanParams, "sampleMetadata", commandOptions.sampleMetadata, true);
+            putNestedIfNotNull(beanParams, "sort", commandOptions.sort, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "outputFileName", commandOptions.outputFileName, true);
+            putNestedIfNotEmpty(beanParams, "outputFileFormat", commandOptions.outputFileFormat, true);
+            putNestedIfNotEmpty(beanParams, "variantsFile", commandOptions.variantsFile, true);
+            putNestedIfNotEmpty(beanParams, "include", commandOptions.bodyInclude, true);
+            putNestedIfNotEmpty(beanParams, "exclude", commandOptions.bodyExclude, true);
+            putNestedIfNotNull(beanParams, "limit", commandOptions.limit, true);
+            putNestedIfNotNull(beanParams, "skip", commandOptions.skip, true);
+            putNestedIfNotNull(beanParams, "summary", commandOptions.summary, true);
 
             variantExportParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -619,10 +619,10 @@ private RestResponse<Job> runFamilyQc() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FamilyQcAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotEmpty(beanParams, "relatednessMethod",commandOptions.relatednessMethod, true);
-            putNestedIfNotEmpty(beanParams, "relatednessMaf",commandOptions.relatednessMaf, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotEmpty(beanParams, "relatednessMethod", commandOptions.relatednessMethod, true);
+            putNestedIfNotEmpty(beanParams, "relatednessMaf", commandOptions.relatednessMaf, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             familyQcAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -684,9 +684,9 @@ private RestResponse<Job> runGatk() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), GatkWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "gatkParams",commandOptions.gatkParams, true);
+            putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "gatkParams", commandOptions.gatkParams, true);
 
             gatkWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -725,11 +725,11 @@ private RestResponse<Job> runGenomePlot() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), GenomePlotAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "configFile",commandOptions.configFile, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "configFile", commandOptions.configFile, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             genomePlotAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -768,18 +768,18 @@ private RestResponse<Job> runGwas() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), GwasAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "phenotype",commandOptions.phenotype, true);
-            putNestedIfNotNull(beanParams, "index",commandOptions.index, true);
-            putNestedIfNotEmpty(beanParams, "indexScoreId",commandOptions.indexScoreId, true);
-            putNestedIfNotNull(beanParams, "method",commandOptions.method, true);
-            putNestedIfNotNull(beanParams, "fisherMode",commandOptions.fisherMode, true);
-            putNestedIfNotEmpty(beanParams, "caseCohort",commandOptions.caseCohort, true);
-            putNestedIfNotEmpty(beanParams, "caseCohortSamplesAnnotation",commandOptions.caseCohortSamplesAnnotation, true);
-            putNestedIfNotNull(beanParams, "caseCohortSamples",commandOptions.caseCohortSamples, true);
-            putNestedIfNotEmpty(beanParams, "controlCohort",commandOptions.controlCohort, true);
-            putNestedIfNotEmpty(beanParams, "controlCohortSamplesAnnotation",commandOptions.controlCohortSamplesAnnotation, true);
-            putNestedIfNotNull(beanParams, "controlCohortSamples",commandOptions.controlCohortSamples, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "phenotype", commandOptions.phenotype, true);
+            putNestedIfNotNull(beanParams, "index", commandOptions.index, true);
+            putNestedIfNotEmpty(beanParams, "indexScoreId", commandOptions.indexScoreId, true);
+            putNestedIfNotNull(beanParams, "method", commandOptions.method, true);
+            putNestedIfNotNull(beanParams, "fisherMode", commandOptions.fisherMode, true);
+            putNestedIfNotEmpty(beanParams, "caseCohort", commandOptions.caseCohort, true);
+            putNestedIfNotEmpty(beanParams, "caseCohortSamplesAnnotation", commandOptions.caseCohortSamplesAnnotation, true);
+            putNestedIfNotNull(beanParams, "caseCohortSamples", commandOptions.caseCohortSamples, true);
+            putNestedIfNotEmpty(beanParams, "controlCohort", commandOptions.controlCohort, true);
+            putNestedIfNotEmpty(beanParams, "controlCohortSamplesAnnotation", commandOptions.controlCohortSamplesAnnotation, true);
+            putNestedIfNotNull(beanParams, "controlCohortSamples", commandOptions.controlCohortSamples, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             gwasAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -818,19 +818,19 @@ private RestResponse<Job> runHrDetect() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), HRDetectAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "sampleId",commandOptions.sampleId, true);
-            putNestedIfNotEmpty(beanParams, "snvFittingId",commandOptions.snvFittingId, true);
-            putNestedIfNotEmpty(beanParams, "svFittingId",commandOptions.svFittingId, true);
-            putNestedIfNotEmpty(beanParams, "cnvQuery",commandOptions.cnvQuery, true);
-            putNestedIfNotEmpty(beanParams, "indelQuery",commandOptions.indelQuery, true);
-            putNestedIfNotEmpty(beanParams, "snv3CustomName",commandOptions.snv3CustomName, true);
-            putNestedIfNotEmpty(beanParams, "snv8CustomName",commandOptions.snv8CustomName, true);
-            putNestedIfNotEmpty(beanParams, "sv3CustomName",commandOptions.sv3CustomName, true);
-            putNestedIfNotEmpty(beanParams, "sv8CustomName",commandOptions.sv8CustomName, true);
-            putNestedIfNotNull(beanParams, "bootstrap",commandOptions.bootstrap, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "sampleId", commandOptions.sampleId, true);
+            putNestedIfNotEmpty(beanParams, "snvFittingId", commandOptions.snvFittingId, true);
+            putNestedIfNotEmpty(beanParams, "svFittingId", commandOptions.svFittingId, true);
+            putNestedIfNotEmpty(beanParams, "cnvQuery", commandOptions.cnvQuery, true);
+            putNestedIfNotEmpty(beanParams, "indelQuery", commandOptions.indelQuery, true);
+            putNestedIfNotEmpty(beanParams, "snv3CustomName", commandOptions.snv3CustomName, true);
+            putNestedIfNotEmpty(beanParams, "snv8CustomName", commandOptions.snv8CustomName, true);
+            putNestedIfNotEmpty(beanParams, "sv3CustomName", commandOptions.sv3CustomName, true);
+            putNestedIfNotEmpty(beanParams, "sv8CustomName", commandOptions.sv8CustomName, true);
+            putNestedIfNotNull(beanParams, "bootstrap", commandOptions.bootstrap, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             hRDetectAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -869,36 +869,36 @@ private RestResponse<Job> runIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "transform",commandOptions.transform, true);
-            putNestedIfNotNull(beanParams, "gvcf",commandOptions.gvcf, true);
-            putNestedIfNotNull(beanParams, "normalizationSkip",commandOptions.normalizationSkip, true);
-            putNestedIfNotEmpty(beanParams, "referenceGenome",commandOptions.referenceGenome, true);
-            putNestedIfNotEmpty(beanParams, "failOnMalformedLines",commandOptions.failOnMalformedLines, true);
-            putNestedIfNotNull(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotNull(beanParams, "somatic",commandOptions.somatic, true);
-            putNestedIfNotNull(beanParams, "load",commandOptions.load, true);
-            putNestedIfNotNull(beanParams, "forceReload",commandOptions.forceReload, true);
-            putNestedIfNotEmpty(beanParams, "loadSplitData",commandOptions.loadSplitData, true);
-            putNestedIfNotNull(beanParams, "loadMultiFileData",commandOptions.loadMultiFileData, true);
-            putNestedIfNotEmpty(beanParams, "loadSampleIndex",commandOptions.loadSampleIndex, true);
-            putNestedIfNotEmpty(beanParams, "loadArchive",commandOptions.loadArchive, true);
-            putNestedIfNotEmpty(beanParams, "loadHomRef",commandOptions.loadHomRef, true);
-            putNestedIfNotEmpty(beanParams, "postLoadCheck",commandOptions.postLoadCheck, true);
-            putNestedIfNotEmpty(beanParams, "includeGenotypes",commandOptions.includeGenotypes, true);
-            putNestedIfNotEmpty(beanParams, "includeSampleData",commandOptions.includeSampleData, true);
-            putNestedIfNotEmpty(beanParams, "merge",commandOptions.merge, true);
-            putNestedIfNotEmpty(beanParams, "deduplicationPolicy",commandOptions.deduplicationPolicy, true);
-            putNestedIfNotNull(beanParams, "calculateStats",commandOptions.calculateStats, true);
-            putNestedIfNotNull(beanParams, "aggregated",commandOptions.aggregated, true);
-            putNestedIfNotEmpty(beanParams, "aggregationMappingFile",commandOptions.aggregationMappingFile, true);
-            putNestedIfNotNull(beanParams, "annotate",commandOptions.annotate, true);
-            putNestedIfNotEmpty(beanParams, "annotator",commandOptions.annotator, true);
-            putNestedIfNotNull(beanParams, "overwriteAnnotations",commandOptions.overwriteAnnotations, true);
-            putNestedIfNotNull(beanParams, "indexSearch",commandOptions.indexSearch, true);
-            putNestedIfNotNull(beanParams, "skipIndexedFiles",commandOptions.skipIndexedFiles, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotNull(beanParams, "transform", commandOptions.transform, true);
+            putNestedIfNotNull(beanParams, "gvcf", commandOptions.gvcf, true);
+            putNestedIfNotNull(beanParams, "normalizationSkip", commandOptions.normalizationSkip, true);
+            putNestedIfNotEmpty(beanParams, "referenceGenome", commandOptions.referenceGenome, true);
+            putNestedIfNotEmpty(beanParams, "failOnMalformedLines", commandOptions.failOnMalformedLines, true);
+            putNestedIfNotNull(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotNull(beanParams, "somatic", commandOptions.somatic, true);
+            putNestedIfNotNull(beanParams, "load", commandOptions.load, true);
+            putNestedIfNotNull(beanParams, "forceReload", commandOptions.forceReload, true);
+            putNestedIfNotEmpty(beanParams, "loadSplitData", commandOptions.loadSplitData, true);
+            putNestedIfNotNull(beanParams, "loadMultiFileData", commandOptions.loadMultiFileData, true);
+            putNestedIfNotEmpty(beanParams, "loadSampleIndex", commandOptions.loadSampleIndex, true);
+            putNestedIfNotEmpty(beanParams, "loadArchive", commandOptions.loadArchive, true);
+            putNestedIfNotEmpty(beanParams, "loadHomRef", commandOptions.loadHomRef, true);
+            putNestedIfNotEmpty(beanParams, "postLoadCheck", commandOptions.postLoadCheck, true);
+            putNestedIfNotEmpty(beanParams, "includeGenotypes", commandOptions.includeGenotypes, true);
+            putNestedIfNotEmpty(beanParams, "includeSampleData", commandOptions.includeSampleData, true);
+            putNestedIfNotEmpty(beanParams, "merge", commandOptions.merge, true);
+            putNestedIfNotEmpty(beanParams, "deduplicationPolicy", commandOptions.deduplicationPolicy, true);
+            putNestedIfNotNull(beanParams, "calculateStats", commandOptions.calculateStats, true);
+            putNestedIfNotNull(beanParams, "aggregated", commandOptions.aggregated, true);
+            putNestedIfNotEmpty(beanParams, "aggregationMappingFile", commandOptions.aggregationMappingFile, true);
+            putNestedIfNotNull(beanParams, "annotate", commandOptions.annotate, true);
+            putNestedIfNotEmpty(beanParams, "annotator", commandOptions.annotator, true);
+            putNestedIfNotNull(beanParams, "overwriteAnnotations", commandOptions.overwriteAnnotations, true);
+            putNestedIfNotNull(beanParams, "indexSearch", commandOptions.indexSearch, true);
+            putNestedIfNotNull(beanParams, "skipIndexedFiles", commandOptions.skipIndexedFiles, true);
 
             variantIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -937,10 +937,10 @@ private RestResponse<Job> runIndividualQc() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), IndividualQcAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "inferredSexMethod",commandOptions.inferredSexMethod, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "inferredSexMethod", commandOptions.inferredSexMethod, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             individualQcAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -979,9 +979,9 @@ private RestResponse<Job> runInferredSex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), InferredSexAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             inferredSexAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1054,16 +1054,16 @@ private RestResponse<Job> runKnockout() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), KnockoutAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "gene",commandOptions.gene, true);
-            putNestedIfNotNull(beanParams, "panel",commandOptions.panel, true);
-            putNestedIfNotEmpty(beanParams, "biotype",commandOptions.biotype, true);
-            putNestedIfNotEmpty(beanParams, "consequenceType",commandOptions.consequenceType, true);
-            putNestedIfNotEmpty(beanParams, "filter",commandOptions.filter, true);
-            putNestedIfNotEmpty(beanParams, "qual",commandOptions.qual, true);
-            putNestedIfNotNull(beanParams, "skipGenesFile",commandOptions.skipGenesFile, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "index",commandOptions.index, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "gene", commandOptions.gene, true);
+            putNestedIfNotNull(beanParams, "panel", commandOptions.panel, true);
+            putNestedIfNotEmpty(beanParams, "biotype", commandOptions.biotype, true);
+            putNestedIfNotEmpty(beanParams, "consequenceType", commandOptions.consequenceType, true);
+            putNestedIfNotEmpty(beanParams, "filter", commandOptions.filter, true);
+            putNestedIfNotEmpty(beanParams, "qual", commandOptions.qual, true);
+            putNestedIfNotNull(beanParams, "skipGenesFile", commandOptions.skipGenesFile, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotNull(beanParams, "index", commandOptions.index, true);
 
             knockoutAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1102,10 +1102,10 @@ private RestResponse<Job> runMendelianError() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), MendelianErrorAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotEmpty(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotEmpty(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             mendelianErrorAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1197,22 +1197,22 @@ private RestResponse<Job> runMutationalSignature() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), MutationalSignatureAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "query",commandOptions.query, true);
-            putNestedIfNotEmpty(beanParams, "fitId",commandOptions.fitId, true);
-            putNestedIfNotEmpty(beanParams, "fitMethod",commandOptions.fitMethod, true);
-            putNestedIfNotNull(beanParams, "fitNBoot",commandOptions.fitNBoot, true);
-            putNestedIfNotEmpty(beanParams, "fitSigVersion",commandOptions.fitSigVersion, true);
-            putNestedIfNotEmpty(beanParams, "fitOrgan",commandOptions.fitOrgan, true);
-            putNestedIfNotNull(beanParams, "fitThresholdPerc",commandOptions.fitThresholdPerc, true);
-            putNestedIfNotNull(beanParams, "fitThresholdPval",commandOptions.fitThresholdPval, true);
-            putNestedIfNotNull(beanParams, "fitMaxRareSigs",commandOptions.fitMaxRareSigs, true);
-            putNestedIfNotEmpty(beanParams, "fitSignaturesFile",commandOptions.fitSignaturesFile, true);
-            putNestedIfNotEmpty(beanParams, "fitRareSignaturesFile",commandOptions.fitRareSignaturesFile, true);
-            putNestedIfNotEmpty(beanParams, "skip",commandOptions.skip, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "query", commandOptions.query, true);
+            putNestedIfNotEmpty(beanParams, "fitId", commandOptions.fitId, true);
+            putNestedIfNotEmpty(beanParams, "fitMethod", commandOptions.fitMethod, true);
+            putNestedIfNotNull(beanParams, "fitNBoot", commandOptions.fitNBoot, true);
+            putNestedIfNotEmpty(beanParams, "fitSigVersion", commandOptions.fitSigVersion, true);
+            putNestedIfNotEmpty(beanParams, "fitOrgan", commandOptions.fitOrgan, true);
+            putNestedIfNotNull(beanParams, "fitThresholdPerc", commandOptions.fitThresholdPerc, true);
+            putNestedIfNotNull(beanParams, "fitThresholdPval", commandOptions.fitThresholdPval, true);
+            putNestedIfNotNull(beanParams, "fitMaxRareSigs", commandOptions.fitMaxRareSigs, true);
+            putNestedIfNotEmpty(beanParams, "fitSignaturesFile", commandOptions.fitSignaturesFile, true);
+            putNestedIfNotEmpty(beanParams, "fitRareSignaturesFile", commandOptions.fitRareSignaturesFile, true);
+            putNestedIfNotEmpty(beanParams, "skip", commandOptions.skip, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             mutationalSignatureAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1251,8 +1251,8 @@ private RestResponse<Job> runPlink() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PlinkWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "plinkParams",commandOptions.plinkParams, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "plinkParams", commandOptions.plinkParams, true);
 
             plinkWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1381,11 +1381,11 @@ private RestResponse<Job> runRelatedness() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), RelatednessAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "individuals",commandOptions.individuals, true);
-            putNestedIfNotNull(beanParams, "samples",commandOptions.samples, true);
-            putNestedIfNotEmpty(beanParams, "minorAlleleFreq",commandOptions.minorAlleleFreq, true);
-            putNestedIfNotEmpty(beanParams, "method",commandOptions.method, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotNull(beanParams, "individuals", commandOptions.individuals, true);
+            putNestedIfNotNull(beanParams, "samples", commandOptions.samples, true);
+            putNestedIfNotEmpty(beanParams, "minorAlleleFreq", commandOptions.minorAlleleFreq, true);
+            putNestedIfNotEmpty(beanParams, "method", commandOptions.method, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             relatednessAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1424,9 +1424,9 @@ private RestResponse<Job> runRvtests() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), RvtestsWrapperParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "command",commandOptions.command, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "rvtestsParams",commandOptions.rvtestsParams, true);
+            putNestedIfNotEmpty(beanParams, "command", commandOptions.command, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedMapIfNotEmpty(beanParams, "rvtestsParams", commandOptions.rvtestsParams, true);
 
             rvtestsWrapperParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1500,9 +1500,9 @@ private RestResponse<Job> runSampleEligibility() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleEligibilityAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "query",commandOptions.query, true);
-            putNestedIfNotNull(beanParams, "index",commandOptions.index, true);
-            putNestedIfNotEmpty(beanParams, "cohortId",commandOptions.cohortId, true);
+            putNestedIfNotEmpty(beanParams, "query", commandOptions.query, true);
+            putNestedIfNotNull(beanParams, "index", commandOptions.index, true);
+            putNestedIfNotEmpty(beanParams, "cohortId", commandOptions.cohortId, true);
 
             sampleEligibilityAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1541,53 +1541,53 @@ private RestResponse<Job> runSampleQc() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleQcAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "vsId",commandOptions.vsId, true);
-            putNestedIfNotEmpty(beanParams, "vsDescription",commandOptions.vsDescription, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.id",commandOptions.vsQueryId, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.region",commandOptions.vsQueryRegion, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.gene",commandOptions.vsQueryGene, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.type",commandOptions.vsQueryType, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.panel",commandOptions.vsQueryPanel, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.panelModeOfInheritance",commandOptions.vsQueryPanelModeOfInheritance, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.panelConfidence",commandOptions.vsQueryPanelConfidence, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.panelRoleInCancer",commandOptions.vsQueryPanelRoleInCancer, true);
-            putNestedIfNotNull(beanParams, "vsQuery.panelIntersection",commandOptions.vsQueryPanelIntersection, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.panelFeatureType",commandOptions.vsQueryPanelFeatureType, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.cohortStatsRef",commandOptions.vsQueryCohortStatsRef, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.cohortStatsAlt",commandOptions.vsQueryCohortStatsAlt, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.cohortStatsMaf",commandOptions.vsQueryCohortStatsMaf, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.ct",commandOptions.vsQueryCt, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.xref",commandOptions.vsQueryXref, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.biotype",commandOptions.vsQueryBiotype, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.proteinSubstitution",commandOptions.vsQueryProteinSubstitution, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.conservation",commandOptions.vsQueryConservation, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.populationFrequencyMaf",commandOptions.vsQueryPopulationFrequencyMaf, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.populationFrequencyAlt",commandOptions.vsQueryPopulationFrequencyAlt, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.populationFrequencyRef",commandOptions.vsQueryPopulationFrequencyRef, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.transcriptFlag",commandOptions.vsQueryTranscriptFlag, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.functionalScore",commandOptions.vsQueryFunctionalScore, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.clinical",commandOptions.vsQueryClinical, true);
-            putNestedIfNotEmpty(beanParams, "vsQuery.clinicalSignificance",commandOptions.vsQueryClinicalSignificance, true);
-            putNestedIfNotNull(beanParams, "vsQuery.clinicalConfirmedStatus",commandOptions.vsQueryClinicalConfirmedStatus, true);
-            putNestedIfNotEmpty(beanParams, "msId",commandOptions.msId, true);
-            putNestedIfNotEmpty(beanParams, "msDescription",commandOptions.msDescription, true);
-            putNestedIfNotEmpty(beanParams, "msQuery",commandOptions.msQuery, true);
-            putNestedIfNotEmpty(beanParams, "msFitId",commandOptions.msFitId, true);
-            putNestedIfNotEmpty(beanParams, "msFitMethod",commandOptions.msFitMethod, true);
-            putNestedIfNotNull(beanParams, "msFitNBoot",commandOptions.msFitNBoot, true);
-            putNestedIfNotEmpty(beanParams, "msFitSigVersion",commandOptions.msFitSigVersion, true);
-            putNestedIfNotEmpty(beanParams, "msFitOrgan",commandOptions.msFitOrgan, true);
-            putNestedIfNotNull(beanParams, "msFitThresholdPerc",commandOptions.msFitThresholdPerc, true);
-            putNestedIfNotNull(beanParams, "msFitThresholdPval",commandOptions.msFitThresholdPval, true);
-            putNestedIfNotNull(beanParams, "msFitMaxRareSigs",commandOptions.msFitMaxRareSigs, true);
-            putNestedIfNotEmpty(beanParams, "msFitSignaturesFile",commandOptions.msFitSignaturesFile, true);
-            putNestedIfNotEmpty(beanParams, "msFitRareSignaturesFile",commandOptions.msFitRareSignaturesFile, true);
-            putNestedIfNotEmpty(beanParams, "gpId",commandOptions.gpId, true);
-            putNestedIfNotEmpty(beanParams, "gpDescription",commandOptions.gpDescription, true);
-            putNestedIfNotEmpty(beanParams, "gpConfigFile",commandOptions.gpConfigFile, true);
-            putNestedIfNotEmpty(beanParams, "skip",commandOptions.skip, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "vsId", commandOptions.vsId, true);
+            putNestedIfNotEmpty(beanParams, "vsDescription", commandOptions.vsDescription, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.id", commandOptions.vsQueryId, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.region", commandOptions.vsQueryRegion, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.gene", commandOptions.vsQueryGene, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.type", commandOptions.vsQueryType, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.panel", commandOptions.vsQueryPanel, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.panelModeOfInheritance", commandOptions.vsQueryPanelModeOfInheritance, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.panelConfidence", commandOptions.vsQueryPanelConfidence, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.panelRoleInCancer", commandOptions.vsQueryPanelRoleInCancer, true);
+            putNestedIfNotNull(beanParams, "vsQuery.panelIntersection", commandOptions.vsQueryPanelIntersection, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.panelFeatureType", commandOptions.vsQueryPanelFeatureType, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.cohortStatsRef", commandOptions.vsQueryCohortStatsRef, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.cohortStatsAlt", commandOptions.vsQueryCohortStatsAlt, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.cohortStatsMaf", commandOptions.vsQueryCohortStatsMaf, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.ct", commandOptions.vsQueryCt, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.xref", commandOptions.vsQueryXref, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.biotype", commandOptions.vsQueryBiotype, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.proteinSubstitution", commandOptions.vsQueryProteinSubstitution, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.conservation", commandOptions.vsQueryConservation, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.populationFrequencyMaf", commandOptions.vsQueryPopulationFrequencyMaf, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.populationFrequencyAlt", commandOptions.vsQueryPopulationFrequencyAlt, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.populationFrequencyRef", commandOptions.vsQueryPopulationFrequencyRef, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.transcriptFlag", commandOptions.vsQueryTranscriptFlag, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.functionalScore", commandOptions.vsQueryFunctionalScore, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.clinical", commandOptions.vsQueryClinical, true);
+            putNestedIfNotEmpty(beanParams, "vsQuery.clinicalSignificance", commandOptions.vsQueryClinicalSignificance, true);
+            putNestedIfNotNull(beanParams, "vsQuery.clinicalConfirmedStatus", commandOptions.vsQueryClinicalConfirmedStatus, true);
+            putNestedIfNotEmpty(beanParams, "msId", commandOptions.msId, true);
+            putNestedIfNotEmpty(beanParams, "msDescription", commandOptions.msDescription, true);
+            putNestedIfNotEmpty(beanParams, "msQuery", commandOptions.msQuery, true);
+            putNestedIfNotEmpty(beanParams, "msFitId", commandOptions.msFitId, true);
+            putNestedIfNotEmpty(beanParams, "msFitMethod", commandOptions.msFitMethod, true);
+            putNestedIfNotNull(beanParams, "msFitNBoot", commandOptions.msFitNBoot, true);
+            putNestedIfNotEmpty(beanParams, "msFitSigVersion", commandOptions.msFitSigVersion, true);
+            putNestedIfNotEmpty(beanParams, "msFitOrgan", commandOptions.msFitOrgan, true);
+            putNestedIfNotNull(beanParams, "msFitThresholdPerc", commandOptions.msFitThresholdPerc, true);
+            putNestedIfNotNull(beanParams, "msFitThresholdPval", commandOptions.msFitThresholdPval, true);
+            putNestedIfNotNull(beanParams, "msFitMaxRareSigs", commandOptions.msFitMaxRareSigs, true);
+            putNestedIfNotEmpty(beanParams, "msFitSignaturesFile", commandOptions.msFitSignaturesFile, true);
+            putNestedIfNotEmpty(beanParams, "msFitRareSignaturesFile", commandOptions.msFitRareSignaturesFile, true);
+            putNestedIfNotEmpty(beanParams, "gpId", commandOptions.gpId, true);
+            putNestedIfNotEmpty(beanParams, "gpDescription", commandOptions.gpDescription, true);
+            putNestedIfNotEmpty(beanParams, "gpConfigFile", commandOptions.gpConfigFile, true);
+            putNestedIfNotEmpty(beanParams, "skip", commandOptions.skip, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             sampleQcAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1644,36 +1644,36 @@ private RestResponse<Job> runSample() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleVariantFilterParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotEmpty(beanParams, "gene",commandOptions.gene, true);
-            putNestedIfNotEmpty(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "panel",commandOptions.panel, true);
-            putNestedIfNotEmpty(beanParams, "panelModeOfInheritance",commandOptions.panelModeOfInheritance, true);
-            putNestedIfNotEmpty(beanParams, "panelConfidence",commandOptions.panelConfidence, true);
-            putNestedIfNotEmpty(beanParams, "panelRoleInCancer",commandOptions.panelRoleInCancer, true);
-            putNestedIfNotNull(beanParams, "panelIntersection",commandOptions.panelIntersection, true);
-            putNestedIfNotEmpty(beanParams, "panelFeatureType",commandOptions.panelFeatureType, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsRef",commandOptions.cohortStatsRef, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsAlt",commandOptions.cohortStatsAlt, true);
-            putNestedIfNotEmpty(beanParams, "cohortStatsMaf",commandOptions.cohortStatsMaf, true);
-            putNestedIfNotEmpty(beanParams, "ct",commandOptions.ct, true);
-            putNestedIfNotEmpty(beanParams, "xref",commandOptions.xref, true);
-            putNestedIfNotEmpty(beanParams, "biotype",commandOptions.biotype, true);
-            putNestedIfNotEmpty(beanParams, "proteinSubstitution",commandOptions.proteinSubstitution, true);
-            putNestedIfNotEmpty(beanParams, "conservation",commandOptions.conservation, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyMaf",commandOptions.populationFrequencyMaf, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyAlt",commandOptions.populationFrequencyAlt, true);
-            putNestedIfNotEmpty(beanParams, "populationFrequencyRef",commandOptions.populationFrequencyRef, true);
-            putNestedIfNotEmpty(beanParams, "transcriptFlag",commandOptions.transcriptFlag, true);
-            putNestedIfNotEmpty(beanParams, "functionalScore",commandOptions.functionalScore, true);
-            putNestedIfNotEmpty(beanParams, "clinical",commandOptions.clinical, true);
-            putNestedIfNotEmpty(beanParams, "clinicalSignificance",commandOptions.clinicalSignificance, true);
-            putNestedIfNotNull(beanParams, "clinicalConfirmedStatus",commandOptions.clinicalConfirmedStatus, true);
-            putNestedIfNotNull(beanParams, "genotypes",commandOptions.genotypes, true);
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "samplesInAllVariants",commandOptions.samplesInAllVariants, true);
-            putNestedIfNotNull(beanParams, "maxVariants",commandOptions.maxVariants, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotEmpty(beanParams, "gene", commandOptions.gene, true);
+            putNestedIfNotEmpty(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "panel", commandOptions.panel, true);
+            putNestedIfNotEmpty(beanParams, "panelModeOfInheritance", commandOptions.panelModeOfInheritance, true);
+            putNestedIfNotEmpty(beanParams, "panelConfidence", commandOptions.panelConfidence, true);
+            putNestedIfNotEmpty(beanParams, "panelRoleInCancer", commandOptions.panelRoleInCancer, true);
+            putNestedIfNotNull(beanParams, "panelIntersection", commandOptions.panelIntersection, true);
+            putNestedIfNotEmpty(beanParams, "panelFeatureType", commandOptions.panelFeatureType, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsRef", commandOptions.cohortStatsRef, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsAlt", commandOptions.cohortStatsAlt, true);
+            putNestedIfNotEmpty(beanParams, "cohortStatsMaf", commandOptions.cohortStatsMaf, true);
+            putNestedIfNotEmpty(beanParams, "ct", commandOptions.ct, true);
+            putNestedIfNotEmpty(beanParams, "xref", commandOptions.xref, true);
+            putNestedIfNotEmpty(beanParams, "biotype", commandOptions.biotype, true);
+            putNestedIfNotEmpty(beanParams, "proteinSubstitution", commandOptions.proteinSubstitution, true);
+            putNestedIfNotEmpty(beanParams, "conservation", commandOptions.conservation, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyMaf", commandOptions.populationFrequencyMaf, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyAlt", commandOptions.populationFrequencyAlt, true);
+            putNestedIfNotEmpty(beanParams, "populationFrequencyRef", commandOptions.populationFrequencyRef, true);
+            putNestedIfNotEmpty(beanParams, "transcriptFlag", commandOptions.transcriptFlag, true);
+            putNestedIfNotEmpty(beanParams, "functionalScore", commandOptions.functionalScore, true);
+            putNestedIfNotEmpty(beanParams, "clinical", commandOptions.clinical, true);
+            putNestedIfNotEmpty(beanParams, "clinicalSignificance", commandOptions.clinicalSignificance, true);
+            putNestedIfNotNull(beanParams, "clinicalConfirmedStatus", commandOptions.clinicalConfirmedStatus, true);
+            putNestedIfNotNull(beanParams, "genotypes", commandOptions.genotypes, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "samplesInAllVariants", commandOptions.samplesInAllVariants, true);
+            putNestedIfNotNull(beanParams, "maxVariants", commandOptions.maxVariants, true);
 
             sampleVariantFilterParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1740,42 +1740,42 @@ private RestResponse<Job> runSampleStats() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleVariantStatsAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.id",commandOptions.variantQueryId, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.region",commandOptions.variantQueryRegion, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.gene",commandOptions.variantQueryGene, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.type",commandOptions.variantQueryType, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.panel",commandOptions.variantQueryPanel, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.panelModeOfInheritance",commandOptions.variantQueryPanelModeOfInheritance, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.panelConfidence",commandOptions.variantQueryPanelConfidence, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.panelRoleInCancer",commandOptions.variantQueryPanelRoleInCancer, true);
-            putNestedIfNotNull(beanParams, "variantQuery.panelIntersection",commandOptions.variantQueryPanelIntersection, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.panelFeatureType",commandOptions.variantQueryPanelFeatureType, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.cohortStatsRef",commandOptions.variantQueryCohortStatsRef, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.cohortStatsAlt",commandOptions.variantQueryCohortStatsAlt, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.cohortStatsMaf",commandOptions.variantQueryCohortStatsMaf, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.ct",commandOptions.variantQueryCt, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.xref",commandOptions.variantQueryXref, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.biotype",commandOptions.variantQueryBiotype, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.proteinSubstitution",commandOptions.variantQueryProteinSubstitution, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.conservation",commandOptions.variantQueryConservation, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.populationFrequencyMaf",commandOptions.variantQueryPopulationFrequencyMaf, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.populationFrequencyAlt",commandOptions.variantQueryPopulationFrequencyAlt, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.populationFrequencyRef",commandOptions.variantQueryPopulationFrequencyRef, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.transcriptFlag",commandOptions.variantQueryTranscriptFlag, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.functionalScore",commandOptions.variantQueryFunctionalScore, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.clinical",commandOptions.variantQueryClinical, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.clinicalSignificance",commandOptions.variantQueryClinicalSignificance, true);
-            putNestedIfNotNull(beanParams, "variantQuery.clinicalConfirmedStatus",commandOptions.variantQueryClinicalConfirmedStatus, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.sampleData",commandOptions.variantQuerySampleData, true);
-            putNestedIfNotEmpty(beanParams, "variantQuery.fileData",commandOptions.variantQueryFileData, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "index",commandOptions.index, true);
-            putNestedIfNotNull(beanParams, "indexOverwrite",commandOptions.indexOverwrite, true);
-            putNestedIfNotEmpty(beanParams, "indexId",commandOptions.indexId, true);
-            putNestedIfNotEmpty(beanParams, "indexDescription",commandOptions.indexDescription, true);
-            putNestedIfNotNull(beanParams, "batchSize",commandOptions.batchSize, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.id", commandOptions.variantQueryId, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.region", commandOptions.variantQueryRegion, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.gene", commandOptions.variantQueryGene, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.type", commandOptions.variantQueryType, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.panel", commandOptions.variantQueryPanel, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.panelModeOfInheritance", commandOptions.variantQueryPanelModeOfInheritance, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.panelConfidence", commandOptions.variantQueryPanelConfidence, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.panelRoleInCancer", commandOptions.variantQueryPanelRoleInCancer, true);
+            putNestedIfNotNull(beanParams, "variantQuery.panelIntersection", commandOptions.variantQueryPanelIntersection, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.panelFeatureType", commandOptions.variantQueryPanelFeatureType, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.cohortStatsRef", commandOptions.variantQueryCohortStatsRef, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.cohortStatsAlt", commandOptions.variantQueryCohortStatsAlt, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.cohortStatsMaf", commandOptions.variantQueryCohortStatsMaf, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.ct", commandOptions.variantQueryCt, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.xref", commandOptions.variantQueryXref, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.biotype", commandOptions.variantQueryBiotype, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.proteinSubstitution", commandOptions.variantQueryProteinSubstitution, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.conservation", commandOptions.variantQueryConservation, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.populationFrequencyMaf", commandOptions.variantQueryPopulationFrequencyMaf, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.populationFrequencyAlt", commandOptions.variantQueryPopulationFrequencyAlt, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.populationFrequencyRef", commandOptions.variantQueryPopulationFrequencyRef, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.transcriptFlag", commandOptions.variantQueryTranscriptFlag, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.functionalScore", commandOptions.variantQueryFunctionalScore, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.clinical", commandOptions.variantQueryClinical, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.clinicalSignificance", commandOptions.variantQueryClinicalSignificance, true);
+            putNestedIfNotNull(beanParams, "variantQuery.clinicalConfirmedStatus", commandOptions.variantQueryClinicalConfirmedStatus, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.sampleData", commandOptions.variantQuerySampleData, true);
+            putNestedIfNotEmpty(beanParams, "variantQuery.fileData", commandOptions.variantQueryFileData, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotNull(beanParams, "index", commandOptions.index, true);
+            putNestedIfNotNull(beanParams, "indexOverwrite", commandOptions.indexOverwrite, true);
+            putNestedIfNotEmpty(beanParams, "indexId", commandOptions.indexId, true);
+            putNestedIfNotEmpty(beanParams, "indexDescription", commandOptions.indexDescription, true);
+            putNestedIfNotNull(beanParams, "batchSize", commandOptions.batchSize, true);
 
             sampleVariantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1815,11 +1815,11 @@ private RestResponse<Job> runStatsExport() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStatsExportParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "cohorts",commandOptions.cohorts, true);
-            putNestedIfNotEmpty(beanParams, "output",commandOptions.output, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotEmpty(beanParams, "gene",commandOptions.gene, true);
-            putNestedIfNotEmpty(beanParams, "outputFileFormat",commandOptions.outputFileFormat, true);
+            putNestedIfNotNull(beanParams, "cohorts", commandOptions.cohorts, true);
+            putNestedIfNotEmpty(beanParams, "output", commandOptions.output, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotEmpty(beanParams, "gene", commandOptions.gene, true);
+            putNestedIfNotEmpty(beanParams, "outputFileFormat", commandOptions.outputFileFormat, true);
 
             variantStatsExportParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1858,14 +1858,14 @@ private RestResponse<Job> runStats() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStatsAnalysisParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "cohort",commandOptions.cohort, true);
-            putNestedIfNotNull(beanParams, "samples",commandOptions.samples, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotEmpty(beanParams, "gene",commandOptions.gene, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotEmpty(beanParams, "outputFileName",commandOptions.outputFileName, true);
-            putNestedIfNotNull(beanParams, "aggregated",commandOptions.aggregated, true);
-            putNestedIfNotEmpty(beanParams, "aggregationMappingFile",commandOptions.aggregationMappingFile, true);
+            putNestedIfNotNull(beanParams, "cohort", commandOptions.cohort, true);
+            putNestedIfNotNull(beanParams, "samples", commandOptions.samples, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotEmpty(beanParams, "gene", commandOptions.gene, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "outputFileName", commandOptions.outputFileName, true);
+            putNestedIfNotNull(beanParams, "aggregated", commandOptions.aggregated, true);
+            putNestedIfNotEmpty(beanParams, "aggregationMappingFile", commandOptions.aggregationMappingFile, true);
 
             variantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java
index b240857de8..287c2223a0 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java
@@ -128,8 +128,8 @@ private RestResponse<CohortAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CohortAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "cohort",commandOptions.cohort, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "cohort", commandOptions.cohort, true);
 
             cohortAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -163,7 +163,7 @@ private RestResponse<Job> loadAnnotationSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TsvAnnotationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
 
             tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -200,16 +200,16 @@ private RestResponse<Cohort> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CohortCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
 
             cohortCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -285,16 +285,16 @@ private RestResponse<Cohort> generate() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CohortGenerateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.bodyId, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.bodyCreationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.bodyModificationDate, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.bodyId, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.bodyCreationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.bodyModificationDate, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             cohortGenerateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -411,16 +411,16 @@ private RestResponse<Cohort> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CohortUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
 
             cohortUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java
index 00dbbbc130..d2fde239e7 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java
@@ -117,8 +117,8 @@ private RestResponse<PanelAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PanelAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "panel",commandOptions.panel, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "panel", commandOptions.panel, true);
 
             panelAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -153,17 +153,17 @@ private RestResponse<Panel> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PanelCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "author",commandOptions.author, true);
-            putNestedIfNotEmpty(beanParams, "source.id",commandOptions.sourceId, true);
-            putNestedIfNotEmpty(beanParams, "source.name",commandOptions.sourceName, true);
-            putNestedIfNotEmpty(beanParams, "source.version",commandOptions.sourceVersion, true);
-            putNestedIfNotEmpty(beanParams, "source.author",commandOptions.sourceAuthor, true);
-            putNestedIfNotEmpty(beanParams, "source.project",commandOptions.sourceProject, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "author", commandOptions.author, true);
+            putNestedIfNotEmpty(beanParams, "source.id", commandOptions.sourceId, true);
+            putNestedIfNotEmpty(beanParams, "source.name", commandOptions.sourceName, true);
+            putNestedIfNotEmpty(beanParams, "source.version", commandOptions.sourceVersion, true);
+            putNestedIfNotEmpty(beanParams, "source.author", commandOptions.sourceAuthor, true);
+            putNestedIfNotEmpty(beanParams, "source.project", commandOptions.sourceProject, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             panelCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -234,8 +234,8 @@ private RestResponse<Job> importPanels() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PanelImportParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "source",commandOptions.source, true);
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "source", commandOptions.source, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
 
             panelImportParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -355,17 +355,17 @@ private RestResponse<Panel> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PanelUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "author",commandOptions.author, true);
-            putNestedIfNotEmpty(beanParams, "source.id",commandOptions.sourceId, true);
-            putNestedIfNotEmpty(beanParams, "source.name",commandOptions.sourceName, true);
-            putNestedIfNotEmpty(beanParams, "source.version",commandOptions.sourceVersion, true);
-            putNestedIfNotEmpty(beanParams, "source.author",commandOptions.sourceAuthor, true);
-            putNestedIfNotEmpty(beanParams, "source.project",commandOptions.sourceProject, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "author", commandOptions.author, true);
+            putNestedIfNotEmpty(beanParams, "source.id", commandOptions.sourceId, true);
+            putNestedIfNotEmpty(beanParams, "source.name", commandOptions.sourceName, true);
+            putNestedIfNotEmpty(beanParams, "source.version", commandOptions.sourceVersion, true);
+            putNestedIfNotEmpty(beanParams, "source.author", commandOptions.sourceAuthor, true);
+            putNestedIfNotEmpty(beanParams, "source.project", commandOptions.sourceProject, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             panelUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java
index 5e93767f51..dc5a1878e4 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java
@@ -126,10 +126,10 @@ private RestResponse<FamilyAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FamilyAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotEmpty(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotEmpty(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
 
             familyAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -163,7 +163,7 @@ private RestResponse<Job> loadAnnotationSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TsvAnnotationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
 
             tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -199,16 +199,16 @@ private RestResponse<Family> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FamilyCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "expectedSize",commandOptions.expectedSize, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotNull(beanParams, "expectedSize", commandOptions.expectedSize, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             familyCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -362,17 +362,17 @@ private RestResponse<Family> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FamilyUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "expectedSize",commandOptions.expectedSize, true);
-            putNestedIfNotNull(beanParams, "qualityControl.files",commandOptions.qualityControlFiles, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotNull(beanParams, "expectedSize", commandOptions.expectedSize, true);
+            putNestedIfNotNull(beanParams, "qualityControl.files", commandOptions.qualityControlFiles, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             familyUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java
index f9f6f5fedb..873a16baac 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java
@@ -197,9 +197,9 @@ private RestResponse<FileAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
 
             fileAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -233,7 +233,7 @@ private RestResponse<Job> loadAnnotationSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TsvAnnotationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
 
             tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -273,27 +273,27 @@ private RestResponse<File> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
-            putNestedIfNotEmpty(beanParams, "path",commandOptions.path, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotNull(beanParams, "format",commandOptions.format, true);
-            putNestedIfNotNull(beanParams, "bioformat",commandOptions.bioformat, true);
-            putNestedIfNotNull(beanParams, "sampleIds",commandOptions.sampleIds, true);
-            putNestedIfNotEmpty(beanParams, "software.name",commandOptions.softwareName, true);
-            putNestedIfNotEmpty(beanParams, "software.version",commandOptions.softwareVersion, true);
-            putNestedIfNotEmpty(beanParams, "software.repository",commandOptions.softwareRepository, true);
-            putNestedIfNotEmpty(beanParams, "software.commit",commandOptions.softwareCommit, true);
-            putNestedIfNotEmpty(beanParams, "software.website",commandOptions.softwareWebsite, true);
-            putNestedIfNotNull(beanParams, "software.params",commandOptions.softwareParams, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotEmpty(beanParams, "jobId",commandOptions.jobId, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "path", commandOptions.path, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotNull(beanParams, "format", commandOptions.format, true);
+            putNestedIfNotNull(beanParams, "bioformat", commandOptions.bioformat, true);
+            putNestedIfNotNull(beanParams, "sampleIds", commandOptions.sampleIds, true);
+            putNestedIfNotEmpty(beanParams, "software.name", commandOptions.softwareName, true);
+            putNestedIfNotEmpty(beanParams, "software.version", commandOptions.softwareVersion, true);
+            putNestedIfNotEmpty(beanParams, "software.repository", commandOptions.softwareRepository, true);
+            putNestedIfNotEmpty(beanParams, "software.commit", commandOptions.softwareCommit, true);
+            putNestedIfNotEmpty(beanParams, "software.website", commandOptions.softwareWebsite, true);
+            putNestedMapIfNotEmpty(beanParams, "software.params", commandOptions.softwareParams, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotEmpty(beanParams, "jobId", commandOptions.jobId, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             fileCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -371,8 +371,8 @@ private RestResponse<Job> fetch() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileFetch.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "url",commandOptions.url, true);
-            putNestedIfNotEmpty(beanParams, "path",commandOptions.path, true);
+            putNestedIfNotEmpty(beanParams, "url", commandOptions.url, true);
+            putNestedIfNotEmpty(beanParams, "path", commandOptions.path, true);
 
             fileFetch = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -412,16 +412,16 @@ private RestResponse<File> link() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileLinkParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "uri",commandOptions.uri, true);
-            putNestedIfNotEmpty(beanParams, "path",commandOptions.path, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "virtualFileName",commandOptions.virtualFileName, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "internal.sampleMap",commandOptions.internalSampleMap, true);
+            putNestedIfNotEmpty(beanParams, "uri", commandOptions.uri, true);
+            putNestedIfNotEmpty(beanParams, "path", commandOptions.path, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "virtualFileName", commandOptions.virtualFileName, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "internal.sampleMap", commandOptions.internalSampleMap, true);
 
             fileLinkParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -460,12 +460,12 @@ private RestResponse<Job> runLink() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileLinkToolParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "uri",commandOptions.uri, true);
-            putNestedIfNotEmpty(beanParams, "path",commandOptions.path, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "virtualFileName",commandOptions.virtualFileName, true);
-            putNestedIfNotNull(beanParams, "parents",commandOptions.parents, true);
-            putNestedIfNotNull(beanParams, "skipPostLink",commandOptions.skipPostLink, true);
+            putNestedIfNotNull(beanParams, "uri", commandOptions.uri, true);
+            putNestedIfNotEmpty(beanParams, "path", commandOptions.path, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "virtualFileName", commandOptions.virtualFileName, true);
+            putNestedIfNotNull(beanParams, "parents", commandOptions.parents, true);
+            putNestedIfNotNull(beanParams, "skipPostLink", commandOptions.skipPostLink, true);
 
             fileLinkToolParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -504,8 +504,8 @@ private RestResponse<Job> runPostlink() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PostLinkToolParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "files",commandOptions.files, true);
-            putNestedIfNotNull(beanParams, "batchSize",commandOptions.batchSize, true);
+            putNestedIfNotNull(beanParams, "files", commandOptions.files, true);
+            putNestedIfNotNull(beanParams, "batchSize", commandOptions.batchSize, true);
 
             postLinkToolParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -669,37 +669,37 @@ private RestResponse<File> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "sampleIds",commandOptions.sampleIds, true);
-            putNestedIfNotNull(beanParams, "format",commandOptions.format, true);
-            putNestedIfNotNull(beanParams, "bioformat",commandOptions.bioformat, true);
-            putNestedIfNotEmpty(beanParams, "software.name",commandOptions.softwareName, true);
-            putNestedIfNotEmpty(beanParams, "software.version",commandOptions.softwareVersion, true);
-            putNestedIfNotEmpty(beanParams, "software.repository",commandOptions.softwareRepository, true);
-            putNestedIfNotEmpty(beanParams, "software.commit",commandOptions.softwareCommit, true);
-            putNestedIfNotEmpty(beanParams, "software.website",commandOptions.softwareWebsite, true);
-            putNestedIfNotNull(beanParams, "software.params",commandOptions.softwareParams, true);
-            putNestedIfNotNull(beanParams, "experiment.technology",commandOptions.experimentTechnology, true);
-            putNestedIfNotNull(beanParams, "experiment.method",commandOptions.experimentMethod, true);
-            putNestedIfNotNull(beanParams, "experiment.nucleicAcidType",commandOptions.experimentNucleicAcidType, true);
-            putNestedIfNotEmpty(beanParams, "experiment.manufacturer",commandOptions.experimentManufacturer, true);
-            putNestedIfNotEmpty(beanParams, "experiment.platform",commandOptions.experimentPlatform, true);
-            putNestedIfNotEmpty(beanParams, "experiment.library",commandOptions.experimentLibrary, true);
-            putNestedIfNotEmpty(beanParams, "experiment.date",commandOptions.experimentDate, true);
-            putNestedIfNotEmpty(beanParams, "experiment.center",commandOptions.experimentCenter, true);
-            putNestedIfNotEmpty(beanParams, "experiment.lab",commandOptions.experimentLab, true);
-            putNestedIfNotEmpty(beanParams, "experiment.responsible",commandOptions.experimentResponsible, true);
-            putNestedIfNotEmpty(beanParams, "experiment.description",commandOptions.experimentDescription, true);
-            putNestedIfNotNull(beanParams, "experiment.attributes",commandOptions.experimentAttributes, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "qualityControl.files",commandOptions.qualityControlFiles, true);
-            putNestedIfNotNull(beanParams, "stats",commandOptions.stats, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotNull(beanParams, "sampleIds", commandOptions.sampleIds, true);
+            putNestedIfNotNull(beanParams, "format", commandOptions.format, true);
+            putNestedIfNotNull(beanParams, "bioformat", commandOptions.bioformat, true);
+            putNestedIfNotEmpty(beanParams, "software.name", commandOptions.softwareName, true);
+            putNestedIfNotEmpty(beanParams, "software.version", commandOptions.softwareVersion, true);
+            putNestedIfNotEmpty(beanParams, "software.repository", commandOptions.softwareRepository, true);
+            putNestedIfNotEmpty(beanParams, "software.commit", commandOptions.softwareCommit, true);
+            putNestedIfNotEmpty(beanParams, "software.website", commandOptions.softwareWebsite, true);
+            putNestedMapIfNotEmpty(beanParams, "software.params", commandOptions.softwareParams, true);
+            putNestedIfNotNull(beanParams, "experiment.technology", commandOptions.experimentTechnology, true);
+            putNestedIfNotNull(beanParams, "experiment.method", commandOptions.experimentMethod, true);
+            putNestedIfNotNull(beanParams, "experiment.nucleicAcidType", commandOptions.experimentNucleicAcidType, true);
+            putNestedIfNotEmpty(beanParams, "experiment.manufacturer", commandOptions.experimentManufacturer, true);
+            putNestedIfNotEmpty(beanParams, "experiment.platform", commandOptions.experimentPlatform, true);
+            putNestedIfNotEmpty(beanParams, "experiment.library", commandOptions.experimentLibrary, true);
+            putNestedIfNotEmpty(beanParams, "experiment.date", commandOptions.experimentDate, true);
+            putNestedIfNotEmpty(beanParams, "experiment.center", commandOptions.experimentCenter, true);
+            putNestedIfNotEmpty(beanParams, "experiment.lab", commandOptions.experimentLab, true);
+            putNestedIfNotEmpty(beanParams, "experiment.responsible", commandOptions.experimentResponsible, true);
+            putNestedIfNotEmpty(beanParams, "experiment.description", commandOptions.experimentDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "experiment.attributes", commandOptions.experimentAttributes, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedIfNotNull(beanParams, "qualityControl.files", commandOptions.qualityControlFiles, true);
+            putNestedMapIfNotEmpty(beanParams, "stats", commandOptions.stats, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             fileUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -820,7 +820,7 @@ private RestResponse<File> move() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), FileMoveParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "path",commandOptions.path, true);
+            putNestedIfNotEmpty(beanParams, "path", commandOptions.path, true);
 
             fileMoveParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java
index 495341543d..dcf24216d8 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java
@@ -135,9 +135,9 @@ private RestResponse<IndividualAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), IndividualAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
 
             individualAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -171,7 +171,7 @@ private RestResponse<Job> loadAnnotationSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TsvAnnotationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
 
             tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -207,42 +207,42 @@ private RestResponse<Individual> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), IndividualCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "father.id",commandOptions.fatherId, true);
-            putNestedIfNotEmpty(beanParams, "father.uuid",commandOptions.fatherUuid, true);
-            putNestedIfNotEmpty(beanParams, "mother.id",commandOptions.motherId, true);
-            putNestedIfNotEmpty(beanParams, "mother.uuid",commandOptions.motherUuid, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "location.address",commandOptions.locationAddress, true);
-            putNestedIfNotEmpty(beanParams, "location.postalCode",commandOptions.locationPostalCode, true);
-            putNestedIfNotEmpty(beanParams, "location.city",commandOptions.locationCity, true);
-            putNestedIfNotEmpty(beanParams, "location.state",commandOptions.locationState, true);
-            putNestedIfNotEmpty(beanParams, "location.country",commandOptions.locationCountry, true);
-            putNestedIfNotEmpty(beanParams, "sex.id",commandOptions.sexId, true);
-            putNestedIfNotEmpty(beanParams, "sex.name",commandOptions.sexName, true);
-            putNestedIfNotEmpty(beanParams, "sex.description",commandOptions.sexDescription, true);
-            putNestedIfNotEmpty(beanParams, "sex.source",commandOptions.sexSource, true);
-            putNestedIfNotEmpty(beanParams, "sex.url",commandOptions.sexUrl, true);
-            putNestedIfNotNull(beanParams, "sex.attributes",commandOptions.sexAttributes, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.id",commandOptions.ethnicityId, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.name",commandOptions.ethnicityName, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.description",commandOptions.ethnicityDescription, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.source",commandOptions.ethnicitySource, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.url",commandOptions.ethnicityUrl, true);
-            putNestedIfNotNull(beanParams, "ethnicity.attributes",commandOptions.ethnicityAttributes, true);
-            putNestedIfNotNull(beanParams, "parentalConsanguinity",commandOptions.parentalConsanguinity, true);
-            putNestedIfNotEmpty(beanParams, "population.name",commandOptions.populationName, true);
-            putNestedIfNotEmpty(beanParams, "population.subpopulation",commandOptions.populationSubpopulation, true);
-            putNestedIfNotEmpty(beanParams, "population.description",commandOptions.populationDescription, true);
-            putNestedIfNotEmpty(beanParams, "dateOfBirth",commandOptions.dateOfBirth, true);
-            putNestedIfNotNull(beanParams, "karyotypicSex",commandOptions.karyotypicSex, true);
-            putNestedIfNotNull(beanParams, "lifeStatus",commandOptions.lifeStatus, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "father.id", commandOptions.fatherId, true);
+            putNestedIfNotEmpty(beanParams, "father.uuid", commandOptions.fatherUuid, true);
+            putNestedIfNotEmpty(beanParams, "mother.id", commandOptions.motherId, true);
+            putNestedIfNotEmpty(beanParams, "mother.uuid", commandOptions.motherUuid, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "location.address", commandOptions.locationAddress, true);
+            putNestedIfNotEmpty(beanParams, "location.postalCode", commandOptions.locationPostalCode, true);
+            putNestedIfNotEmpty(beanParams, "location.city", commandOptions.locationCity, true);
+            putNestedIfNotEmpty(beanParams, "location.state", commandOptions.locationState, true);
+            putNestedIfNotEmpty(beanParams, "location.country", commandOptions.locationCountry, true);
+            putNestedIfNotEmpty(beanParams, "sex.id", commandOptions.sexId, true);
+            putNestedIfNotEmpty(beanParams, "sex.name", commandOptions.sexName, true);
+            putNestedIfNotEmpty(beanParams, "sex.description", commandOptions.sexDescription, true);
+            putNestedIfNotEmpty(beanParams, "sex.source", commandOptions.sexSource, true);
+            putNestedIfNotEmpty(beanParams, "sex.url", commandOptions.sexUrl, true);
+            putNestedMapIfNotEmpty(beanParams, "sex.attributes", commandOptions.sexAttributes, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.id", commandOptions.ethnicityId, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.name", commandOptions.ethnicityName, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.description", commandOptions.ethnicityDescription, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.source", commandOptions.ethnicitySource, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.url", commandOptions.ethnicityUrl, true);
+            putNestedMapIfNotEmpty(beanParams, "ethnicity.attributes", commandOptions.ethnicityAttributes, true);
+            putNestedIfNotNull(beanParams, "parentalConsanguinity", commandOptions.parentalConsanguinity, true);
+            putNestedIfNotEmpty(beanParams, "population.name", commandOptions.populationName, true);
+            putNestedIfNotEmpty(beanParams, "population.subpopulation", commandOptions.populationSubpopulation, true);
+            putNestedIfNotEmpty(beanParams, "population.description", commandOptions.populationDescription, true);
+            putNestedIfNotEmpty(beanParams, "dateOfBirth", commandOptions.dateOfBirth, true);
+            putNestedIfNotNull(beanParams, "karyotypicSex", commandOptions.karyotypicSex, true);
+            putNestedIfNotNull(beanParams, "lifeStatus", commandOptions.lifeStatus, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             individualCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -411,43 +411,43 @@ private RestResponse<Individual> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), IndividualUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "father.id",commandOptions.fatherId, true);
-            putNestedIfNotEmpty(beanParams, "father.uuid",commandOptions.fatherUuid, true);
-            putNestedIfNotEmpty(beanParams, "mother.id",commandOptions.motherId, true);
-            putNestedIfNotEmpty(beanParams, "mother.uuid",commandOptions.motherUuid, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "parentalConsanguinity",commandOptions.parentalConsanguinity, true);
-            putNestedIfNotEmpty(beanParams, "location.address",commandOptions.locationAddress, true);
-            putNestedIfNotEmpty(beanParams, "location.postalCode",commandOptions.locationPostalCode, true);
-            putNestedIfNotEmpty(beanParams, "location.city",commandOptions.locationCity, true);
-            putNestedIfNotEmpty(beanParams, "location.state",commandOptions.locationState, true);
-            putNestedIfNotEmpty(beanParams, "location.country",commandOptions.locationCountry, true);
-            putNestedIfNotEmpty(beanParams, "sex.id",commandOptions.sexId, true);
-            putNestedIfNotEmpty(beanParams, "sex.name",commandOptions.sexName, true);
-            putNestedIfNotEmpty(beanParams, "sex.description",commandOptions.sexDescription, true);
-            putNestedIfNotEmpty(beanParams, "sex.source",commandOptions.sexSource, true);
-            putNestedIfNotEmpty(beanParams, "sex.url",commandOptions.sexUrl, true);
-            putNestedIfNotNull(beanParams, "sex.attributes",commandOptions.sexAttributes, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.id",commandOptions.ethnicityId, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.name",commandOptions.ethnicityName, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.description",commandOptions.ethnicityDescription, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.source",commandOptions.ethnicitySource, true);
-            putNestedIfNotEmpty(beanParams, "ethnicity.url",commandOptions.ethnicityUrl, true);
-            putNestedIfNotNull(beanParams, "ethnicity.attributes",commandOptions.ethnicityAttributes, true);
-            putNestedIfNotEmpty(beanParams, "population.name",commandOptions.populationName, true);
-            putNestedIfNotEmpty(beanParams, "population.subpopulation",commandOptions.populationSubpopulation, true);
-            putNestedIfNotEmpty(beanParams, "population.description",commandOptions.populationDescription, true);
-            putNestedIfNotEmpty(beanParams, "dateOfBirth",commandOptions.dateOfBirth, true);
-            putNestedIfNotNull(beanParams, "karyotypicSex",commandOptions.karyotypicSex, true);
-            putNestedIfNotNull(beanParams, "lifeStatus",commandOptions.lifeStatus, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "qualityControl.files",commandOptions.qualityControlFiles, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "father.id", commandOptions.fatherId, true);
+            putNestedIfNotEmpty(beanParams, "father.uuid", commandOptions.fatherUuid, true);
+            putNestedIfNotEmpty(beanParams, "mother.id", commandOptions.motherId, true);
+            putNestedIfNotEmpty(beanParams, "mother.uuid", commandOptions.motherUuid, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotNull(beanParams, "parentalConsanguinity", commandOptions.parentalConsanguinity, true);
+            putNestedIfNotEmpty(beanParams, "location.address", commandOptions.locationAddress, true);
+            putNestedIfNotEmpty(beanParams, "location.postalCode", commandOptions.locationPostalCode, true);
+            putNestedIfNotEmpty(beanParams, "location.city", commandOptions.locationCity, true);
+            putNestedIfNotEmpty(beanParams, "location.state", commandOptions.locationState, true);
+            putNestedIfNotEmpty(beanParams, "location.country", commandOptions.locationCountry, true);
+            putNestedIfNotEmpty(beanParams, "sex.id", commandOptions.sexId, true);
+            putNestedIfNotEmpty(beanParams, "sex.name", commandOptions.sexName, true);
+            putNestedIfNotEmpty(beanParams, "sex.description", commandOptions.sexDescription, true);
+            putNestedIfNotEmpty(beanParams, "sex.source", commandOptions.sexSource, true);
+            putNestedIfNotEmpty(beanParams, "sex.url", commandOptions.sexUrl, true);
+            putNestedMapIfNotEmpty(beanParams, "sex.attributes", commandOptions.sexAttributes, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.id", commandOptions.ethnicityId, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.name", commandOptions.ethnicityName, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.description", commandOptions.ethnicityDescription, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.source", commandOptions.ethnicitySource, true);
+            putNestedIfNotEmpty(beanParams, "ethnicity.url", commandOptions.ethnicityUrl, true);
+            putNestedMapIfNotEmpty(beanParams, "ethnicity.attributes", commandOptions.ethnicityAttributes, true);
+            putNestedIfNotEmpty(beanParams, "population.name", commandOptions.populationName, true);
+            putNestedIfNotEmpty(beanParams, "population.subpopulation", commandOptions.populationSubpopulation, true);
+            putNestedIfNotEmpty(beanParams, "population.description", commandOptions.populationDescription, true);
+            putNestedIfNotEmpty(beanParams, "dateOfBirth", commandOptions.dateOfBirth, true);
+            putNestedIfNotNull(beanParams, "karyotypicSex", commandOptions.karyotypicSex, true);
+            putNestedIfNotNull(beanParams, "lifeStatus", commandOptions.lifeStatus, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedIfNotNull(beanParams, "qualityControl.files", commandOptions.qualityControlFiles, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             individualUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java
index cf28e7983b..ffc4c7a61a 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java
@@ -137,8 +137,8 @@ private RestResponse<JobAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), JobAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "job",commandOptions.job, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "job", commandOptions.job, true);
 
             jobAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -170,25 +170,25 @@ private RestResponse<Job> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), JobCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "tool.id",commandOptions.toolId, true);
-            putNestedIfNotEmpty(beanParams, "tool.description",commandOptions.toolDescription, true);
-            putNestedIfNotNull(beanParams, "tool.scope",commandOptions.toolScope, true);
-            putNestedIfNotNull(beanParams, "tool.type",commandOptions.toolType, true);
-            putNestedIfNotNull(beanParams, "tool.resource",commandOptions.toolResource, true);
-            putNestedIfNotNull(beanParams, "priority",commandOptions.priority, true);
-            putNestedIfNotEmpty(beanParams, "commandLine",commandOptions.commandLine, true);
-            putNestedIfNotNull(beanParams, "params",commandOptions.params, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "outDir.path",commandOptions.outDirPath, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotEmpty(beanParams, "result.id",commandOptions.resultId, true);
-            putNestedIfNotNull(beanParams, "result.attributes",commandOptions.resultAttributes, true);
-            putNestedIfNotEmpty(beanParams, "stdout.path",commandOptions.stdoutPath, true);
-            putNestedIfNotEmpty(beanParams, "stderr.path",commandOptions.stderrPath, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "tool.id", commandOptions.toolId, true);
+            putNestedIfNotEmpty(beanParams, "tool.description", commandOptions.toolDescription, true);
+            putNestedIfNotNull(beanParams, "tool.scope", commandOptions.toolScope, true);
+            putNestedIfNotNull(beanParams, "tool.type", commandOptions.toolType, true);
+            putNestedIfNotNull(beanParams, "tool.resource", commandOptions.toolResource, true);
+            putNestedIfNotNull(beanParams, "priority", commandOptions.priority, true);
+            putNestedIfNotEmpty(beanParams, "commandLine", commandOptions.commandLine, true);
+            putNestedMapIfNotEmpty(beanParams, "params", commandOptions.params, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "outDir.path", commandOptions.outDirPath, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotEmpty(beanParams, "result.id", commandOptions.resultId, true);
+            putNestedMapIfNotEmpty(beanParams, "result.attributes", commandOptions.resultAttributes, true);
+            putNestedIfNotEmpty(beanParams, "stdout.path", commandOptions.stdoutPath, true);
+            putNestedIfNotEmpty(beanParams, "stderr.path", commandOptions.stderrPath, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             jobCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -257,9 +257,9 @@ private RestResponse<Job> retry() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), JobRetryParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "job",commandOptions.job, true);
-            putNestedIfNotNull(beanParams, "force",commandOptions.force, true);
-            putNestedIfNotNull(beanParams, "params",commandOptions.params, true);
+            putNestedIfNotEmpty(beanParams, "job", commandOptions.job, true);
+            putNestedIfNotNull(beanParams, "force", commandOptions.force, true);
+            putNestedMapIfNotEmpty(beanParams, "params", commandOptions.params, true);
 
             jobRetryParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -392,10 +392,10 @@ private RestResponse<Job> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), JobUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "visited",commandOptions.visited, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotNull(beanParams, "visited", commandOptions.visited, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             jobUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java
index 72f9bdd0e8..f1e0c47ad7 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java
@@ -17,8 +17,8 @@
 package org.opencb.opencga.app.cli.main.executors;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.datastore.core.ObjectMap;
@@ -36,19 +36,13 @@
 import org.opencb.opencga.core.models.user.AuthenticationResponse;
 import org.opencb.opencga.core.response.QueryType;
 import org.opencb.opencga.core.response.RestResponse;
-import org.opencb.opencga.server.generator.models.RestCategory;
-import org.opencb.opencga.server.generator.models.RestEndpoint;
-import org.opencb.opencga.server.generator.models.RestParameter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.lang.reflect.Method;
 import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.Base64;
-import java.util.Date;
-import java.util.List;
+import java.util.*;
 
 /**
  * Created on 27/05/16.
@@ -266,18 +260,22 @@ public RestResponse<AuthenticationResponse> refreshToken(AuthenticationResponse
         return res;
     }
 
-    public Object putNestedIfNotNull(ObjectMap map, String key, Object value, boolean parents) {
+    public void putNestedIfNotNull(ObjectMap map, String key, Object value, boolean parents) {
         if (value != null) {
             map.putNested(key, value, parents);
         }
-        return null;
     }
 
-    public Object putNestedIfNotEmpty(ObjectMap map, String key, String value, boolean parents) {
+    public void putNestedIfNotEmpty(ObjectMap map, String key, String value, boolean parents) {
         if (StringUtils.isNotEmpty(value)) {
             map.putNested(key, value, parents);
         }
-        return null;
+    }
+
+    public void putNestedMapIfNotEmpty(ObjectMap map, String key, Map<String, ?> value, boolean parents) {
+        if (MapUtils.isNotEmpty(value)) {
+            map.putNested(key, value, parents);
+        }
     }
 
     public boolean checkExpiredSession(String[] args) {
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java
index 6135886595..6f351a6b38 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java
@@ -189,10 +189,10 @@ private RestResponse<Job> configureCellbase() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), CellBaseConfiguration.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "url",commandOptions.url, true);
-            putNestedIfNotEmpty(beanParams, "version",commandOptions.version, true);
-            putNestedIfNotEmpty(beanParams, "dataRelease",commandOptions.dataRelease, true);
-            putNestedIfNotEmpty(beanParams, "apiKey",commandOptions.apiKey, true);
+            putNestedIfNotEmpty(beanParams, "url", commandOptions.url, true);
+            putNestedIfNotEmpty(beanParams, "version", commandOptions.version, true);
+            putNestedIfNotEmpty(beanParams, "dataRelease", commandOptions.dataRelease, true);
+            putNestedIfNotEmpty(beanParams, "apiKey", commandOptions.apiKey, true);
 
             cellBaseConfiguration = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -231,8 +231,8 @@ private RestResponse<Job> aggregateVariant() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantAggregateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
 
             variantAggregateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -291,15 +291,15 @@ private RestResponse<Job> indexVariantAnnotation() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantAnnotationIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotEmpty(beanParams, "outputFileName",commandOptions.outputFileName, true);
-            putNestedIfNotEmpty(beanParams, "annotator",commandOptions.annotator, true);
-            putNestedIfNotNull(beanParams, "overwriteAnnotations",commandOptions.overwriteAnnotations, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotNull(beanParams, "create",commandOptions.create, true);
-            putNestedIfNotEmpty(beanParams, "load",commandOptions.load, true);
-            putNestedIfNotEmpty(beanParams, "customName",commandOptions.customName, true);
-            putNestedIfNotNull(beanParams, "sampleIndexAnnotation",commandOptions.sampleIndexAnnotation, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotEmpty(beanParams, "outputFileName", commandOptions.outputFileName, true);
+            putNestedIfNotEmpty(beanParams, "annotator", commandOptions.annotator, true);
+            putNestedIfNotNull(beanParams, "overwriteAnnotations", commandOptions.overwriteAnnotations, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotNull(beanParams, "create", commandOptions.create, true);
+            putNestedIfNotEmpty(beanParams, "load", commandOptions.load, true);
+            putNestedIfNotEmpty(beanParams, "customName", commandOptions.customName, true);
+            putNestedIfNotNull(beanParams, "sampleIndexAnnotation", commandOptions.sampleIndexAnnotation, true);
 
             variantAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -335,7 +335,7 @@ private RestResponse<Job> saveVariantAnnotation() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantAnnotationSaveParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "annotationId",commandOptions.annotationId, true);
+            putNestedIfNotEmpty(beanParams, "annotationId", commandOptions.annotationId, true);
 
             variantAnnotationSaveParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -368,7 +368,7 @@ private RestResponse<ObjectMap> configureVariant() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantConfigureParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "configuration",commandOptions.configuration, true);
+            putNestedMapIfNotEmpty(beanParams, "configuration", commandOptions.configuration, true);
 
             variantConfigureParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -407,9 +407,9 @@ private RestResponse<Job> deleteVariant() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantFileDeleteParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
-            putNestedIfNotNull(beanParams, "force",commandOptions.force, true);
+            putNestedIfNotNull(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
+            putNestedIfNotNull(beanParams, "force", commandOptions.force, true);
 
             variantFileDeleteParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -448,9 +448,9 @@ private RestResponse<Job> aggregateVariantFamily() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantAggregateFamilyParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "samples",commandOptions.samples, true);
-            putNestedIfNotEmpty(beanParams, "gapsGenotype",commandOptions.gapsGenotype, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
+            putNestedIfNotNull(beanParams, "samples", commandOptions.samples, true);
+            putNestedIfNotEmpty(beanParams, "gapsGenotype", commandOptions.gapsGenotype, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
 
             variantAggregateFamilyParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -489,10 +489,10 @@ private RestResponse<Job> indexVariantFamily() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantFamilyIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
-            putNestedIfNotNull(beanParams, "updateIndex",commandOptions.updateIndex, true);
-            putNestedIfNotNull(beanParams, "skipIncompleteFamilies",commandOptions.skipIncompleteFamilies, true);
+            putNestedIfNotNull(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
+            putNestedIfNotNull(beanParams, "updateIndex", commandOptions.updateIndex, true);
+            putNestedIfNotNull(beanParams, "skipIncompleteFamilies", commandOptions.skipIncompleteFamilies, true);
 
             variantFamilyIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -531,36 +531,36 @@ private RestResponse<Job> indexVariant() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
-            putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
-            putNestedIfNotNull(beanParams, "transform",commandOptions.transform, true);
-            putNestedIfNotNull(beanParams, "gvcf",commandOptions.gvcf, true);
-            putNestedIfNotNull(beanParams, "normalizationSkip",commandOptions.normalizationSkip, true);
-            putNestedIfNotEmpty(beanParams, "referenceGenome",commandOptions.referenceGenome, true);
-            putNestedIfNotEmpty(beanParams, "failOnMalformedLines",commandOptions.failOnMalformedLines, true);
-            putNestedIfNotNull(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotNull(beanParams, "somatic",commandOptions.somatic, true);
-            putNestedIfNotNull(beanParams, "load",commandOptions.load, true);
-            putNestedIfNotNull(beanParams, "forceReload",commandOptions.forceReload, true);
-            putNestedIfNotEmpty(beanParams, "loadSplitData",commandOptions.loadSplitData, true);
-            putNestedIfNotNull(beanParams, "loadMultiFileData",commandOptions.loadMultiFileData, true);
-            putNestedIfNotEmpty(beanParams, "loadSampleIndex",commandOptions.loadSampleIndex, true);
-            putNestedIfNotEmpty(beanParams, "loadArchive",commandOptions.loadArchive, true);
-            putNestedIfNotEmpty(beanParams, "loadHomRef",commandOptions.loadHomRef, true);
-            putNestedIfNotEmpty(beanParams, "postLoadCheck",commandOptions.postLoadCheck, true);
-            putNestedIfNotEmpty(beanParams, "includeGenotypes",commandOptions.includeGenotypes, true);
-            putNestedIfNotEmpty(beanParams, "includeSampleData",commandOptions.includeSampleData, true);
-            putNestedIfNotEmpty(beanParams, "merge",commandOptions.merge, true);
-            putNestedIfNotEmpty(beanParams, "deduplicationPolicy",commandOptions.deduplicationPolicy, true);
-            putNestedIfNotNull(beanParams, "calculateStats",commandOptions.calculateStats, true);
-            putNestedIfNotNull(beanParams, "aggregated",commandOptions.aggregated, true);
-            putNestedIfNotEmpty(beanParams, "aggregationMappingFile",commandOptions.aggregationMappingFile, true);
-            putNestedIfNotNull(beanParams, "annotate",commandOptions.annotate, true);
-            putNestedIfNotEmpty(beanParams, "annotator",commandOptions.annotator, true);
-            putNestedIfNotNull(beanParams, "overwriteAnnotations",commandOptions.overwriteAnnotations, true);
-            putNestedIfNotNull(beanParams, "indexSearch",commandOptions.indexSearch, true);
-            putNestedIfNotNull(beanParams, "skipIndexedFiles",commandOptions.skipIndexedFiles, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
+            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
+            putNestedIfNotNull(beanParams, "transform", commandOptions.transform, true);
+            putNestedIfNotNull(beanParams, "gvcf", commandOptions.gvcf, true);
+            putNestedIfNotNull(beanParams, "normalizationSkip", commandOptions.normalizationSkip, true);
+            putNestedIfNotEmpty(beanParams, "referenceGenome", commandOptions.referenceGenome, true);
+            putNestedIfNotEmpty(beanParams, "failOnMalformedLines", commandOptions.failOnMalformedLines, true);
+            putNestedIfNotNull(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotNull(beanParams, "somatic", commandOptions.somatic, true);
+            putNestedIfNotNull(beanParams, "load", commandOptions.load, true);
+            putNestedIfNotNull(beanParams, "forceReload", commandOptions.forceReload, true);
+            putNestedIfNotEmpty(beanParams, "loadSplitData", commandOptions.loadSplitData, true);
+            putNestedIfNotNull(beanParams, "loadMultiFileData", commandOptions.loadMultiFileData, true);
+            putNestedIfNotEmpty(beanParams, "loadSampleIndex", commandOptions.loadSampleIndex, true);
+            putNestedIfNotEmpty(beanParams, "loadArchive", commandOptions.loadArchive, true);
+            putNestedIfNotEmpty(beanParams, "loadHomRef", commandOptions.loadHomRef, true);
+            putNestedIfNotEmpty(beanParams, "postLoadCheck", commandOptions.postLoadCheck, true);
+            putNestedIfNotEmpty(beanParams, "includeGenotypes", commandOptions.includeGenotypes, true);
+            putNestedIfNotEmpty(beanParams, "includeSampleData", commandOptions.includeSampleData, true);
+            putNestedIfNotEmpty(beanParams, "merge", commandOptions.merge, true);
+            putNestedIfNotEmpty(beanParams, "deduplicationPolicy", commandOptions.deduplicationPolicy, true);
+            putNestedIfNotNull(beanParams, "calculateStats", commandOptions.calculateStats, true);
+            putNestedIfNotNull(beanParams, "aggregated", commandOptions.aggregated, true);
+            putNestedIfNotEmpty(beanParams, "aggregationMappingFile", commandOptions.aggregationMappingFile, true);
+            putNestedIfNotNull(beanParams, "annotate", commandOptions.annotate, true);
+            putNestedIfNotEmpty(beanParams, "annotator", commandOptions.annotator, true);
+            putNestedIfNotNull(beanParams, "overwriteAnnotations", commandOptions.overwriteAnnotations, true);
+            putNestedIfNotNull(beanParams, "indexSearch", commandOptions.indexSearch, true);
+            putNestedIfNotNull(beanParams, "skipIndexedFiles", commandOptions.skipIndexedFiles, true);
 
             variantIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -599,41 +599,41 @@ private RestResponse<Job> launcherVariantIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantFileIndexJobLauncherParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "directory",commandOptions.directory, true);
-            putNestedIfNotNull(beanParams, "resumeFailed",commandOptions.resumeFailed, true);
-            putNestedIfNotNull(beanParams, "ignoreFailed",commandOptions.ignoreFailed, true);
-            putNestedIfNotNull(beanParams, "maxJobs",commandOptions.maxJobs, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.file",commandOptions.indexParamsFile, true);
-            putNestedIfNotNull(beanParams, "indexParams.resume",commandOptions.indexParamsResume, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.outdir",commandOptions.indexParamsOutdir, true);
-            putNestedIfNotNull(beanParams, "indexParams.transform",commandOptions.indexParamsTransform, true);
-            putNestedIfNotNull(beanParams, "indexParams.gvcf",commandOptions.indexParamsGvcf, true);
-            putNestedIfNotNull(beanParams, "indexParams.normalizationSkip",commandOptions.indexParamsNormalizationSkip, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.referenceGenome",commandOptions.indexParamsReferenceGenome, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.failOnMalformedLines",commandOptions.indexParamsFailOnMalformedLines, true);
-            putNestedIfNotNull(beanParams, "indexParams.family",commandOptions.indexParamsFamily, true);
-            putNestedIfNotNull(beanParams, "indexParams.somatic",commandOptions.indexParamsSomatic, true);
-            putNestedIfNotNull(beanParams, "indexParams.load",commandOptions.indexParamsLoad, true);
-            putNestedIfNotNull(beanParams, "indexParams.forceReload",commandOptions.indexParamsForceReload, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.loadSplitData",commandOptions.indexParamsLoadSplitData, true);
-            putNestedIfNotNull(beanParams, "indexParams.loadMultiFileData",commandOptions.indexParamsLoadMultiFileData, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.loadSampleIndex",commandOptions.indexParamsLoadSampleIndex, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.loadArchive",commandOptions.indexParamsLoadArchive, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.loadHomRef",commandOptions.indexParamsLoadHomRef, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.postLoadCheck",commandOptions.indexParamsPostLoadCheck, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.includeGenotypes",commandOptions.indexParamsIncludeGenotypes, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.includeSampleData",commandOptions.indexParamsIncludeSampleData, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.merge",commandOptions.indexParamsMerge, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.deduplicationPolicy",commandOptions.indexParamsDeduplicationPolicy, true);
-            putNestedIfNotNull(beanParams, "indexParams.calculateStats",commandOptions.indexParamsCalculateStats, true);
-            putNestedIfNotNull(beanParams, "indexParams.aggregated",commandOptions.indexParamsAggregated, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.aggregationMappingFile",commandOptions.indexParamsAggregationMappingFile, true);
-            putNestedIfNotNull(beanParams, "indexParams.annotate",commandOptions.indexParamsAnnotate, true);
-            putNestedIfNotEmpty(beanParams, "indexParams.annotator",commandOptions.indexParamsAnnotator, true);
-            putNestedIfNotNull(beanParams, "indexParams.overwriteAnnotations",commandOptions.indexParamsOverwriteAnnotations, true);
-            putNestedIfNotNull(beanParams, "indexParams.indexSearch",commandOptions.indexParamsIndexSearch, true);
-            putNestedIfNotNull(beanParams, "indexParams.skipIndexedFiles",commandOptions.indexParamsSkipIndexedFiles, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "directory", commandOptions.directory, true);
+            putNestedIfNotNull(beanParams, "resumeFailed", commandOptions.resumeFailed, true);
+            putNestedIfNotNull(beanParams, "ignoreFailed", commandOptions.ignoreFailed, true);
+            putNestedIfNotNull(beanParams, "maxJobs", commandOptions.maxJobs, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.file", commandOptions.indexParamsFile, true);
+            putNestedIfNotNull(beanParams, "indexParams.resume", commandOptions.indexParamsResume, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.outdir", commandOptions.indexParamsOutdir, true);
+            putNestedIfNotNull(beanParams, "indexParams.transform", commandOptions.indexParamsTransform, true);
+            putNestedIfNotNull(beanParams, "indexParams.gvcf", commandOptions.indexParamsGvcf, true);
+            putNestedIfNotNull(beanParams, "indexParams.normalizationSkip", commandOptions.indexParamsNormalizationSkip, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.referenceGenome", commandOptions.indexParamsReferenceGenome, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.failOnMalformedLines", commandOptions.indexParamsFailOnMalformedLines, true);
+            putNestedIfNotNull(beanParams, "indexParams.family", commandOptions.indexParamsFamily, true);
+            putNestedIfNotNull(beanParams, "indexParams.somatic", commandOptions.indexParamsSomatic, true);
+            putNestedIfNotNull(beanParams, "indexParams.load", commandOptions.indexParamsLoad, true);
+            putNestedIfNotNull(beanParams, "indexParams.forceReload", commandOptions.indexParamsForceReload, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.loadSplitData", commandOptions.indexParamsLoadSplitData, true);
+            putNestedIfNotNull(beanParams, "indexParams.loadMultiFileData", commandOptions.indexParamsLoadMultiFileData, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.loadSampleIndex", commandOptions.indexParamsLoadSampleIndex, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.loadArchive", commandOptions.indexParamsLoadArchive, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.loadHomRef", commandOptions.indexParamsLoadHomRef, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.postLoadCheck", commandOptions.indexParamsPostLoadCheck, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.includeGenotypes", commandOptions.indexParamsIncludeGenotypes, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.includeSampleData", commandOptions.indexParamsIncludeSampleData, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.merge", commandOptions.indexParamsMerge, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.deduplicationPolicy", commandOptions.indexParamsDeduplicationPolicy, true);
+            putNestedIfNotNull(beanParams, "indexParams.calculateStats", commandOptions.indexParamsCalculateStats, true);
+            putNestedIfNotNull(beanParams, "indexParams.aggregated", commandOptions.indexParamsAggregated, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.aggregationMappingFile", commandOptions.indexParamsAggregationMappingFile, true);
+            putNestedIfNotNull(beanParams, "indexParams.annotate", commandOptions.indexParamsAnnotate, true);
+            putNestedIfNotEmpty(beanParams, "indexParams.annotator", commandOptions.indexParamsAnnotator, true);
+            putNestedIfNotNull(beanParams, "indexParams.overwriteAnnotations", commandOptions.indexParamsOverwriteAnnotations, true);
+            putNestedIfNotNull(beanParams, "indexParams.indexSearch", commandOptions.indexParamsIndexSearch, true);
+            putNestedIfNotNull(beanParams, "indexParams.skipIndexedFiles", commandOptions.indexParamsSkipIndexedFiles, true);
 
             variantFileIndexJobLauncherParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -669,9 +669,9 @@ private RestResponse<Job> runVariantJulie() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), JulieParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "cohorts",commandOptions.cohorts, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
+            putNestedIfNotNull(beanParams, "cohorts", commandOptions.cohorts, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
 
             julieParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -706,8 +706,8 @@ private RestResponse<Job> repairVariantMetadata() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStorageMetadataRepairToolParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "studies",commandOptions.studies, true);
-            putNestedIfNotNull(beanParams, "samplesBatchSize",commandOptions.samplesBatchSize, true);
+            putNestedIfNotNull(beanParams, "studies", commandOptions.studies, true);
+            putNestedIfNotNull(beanParams, "samplesBatchSize", commandOptions.samplesBatchSize, true);
 
             variantStorageMetadataRepairToolParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -746,8 +746,8 @@ private RestResponse<Job> synchronizeVariantMetadata() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStorageMetadataSynchronizeParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "study",commandOptions.bodyStudy, true);
-            putNestedIfNotNull(beanParams, "files",commandOptions.files, true);
+            putNestedIfNotEmpty(beanParams, "study", commandOptions.bodyStudy, true);
+            putNestedIfNotNull(beanParams, "files", commandOptions.files, true);
 
             variantStorageMetadataSynchronizeParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -782,9 +782,9 @@ private RestResponse<Job> pruneVariant() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantPruneParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "project",commandOptions.project, true);
-            putNestedIfNotNull(beanParams, "dryRun",commandOptions.dryRun, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
+            putNestedIfNotEmpty(beanParams, "project", commandOptions.project, true);
+            putNestedIfNotNull(beanParams, "dryRun", commandOptions.dryRun, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
 
             variantPruneParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -823,9 +823,9 @@ private RestResponse<Job> deleteVariantSample() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantSampleDeleteParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "force",commandOptions.force, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "force", commandOptions.force, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
 
             variantSampleDeleteParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -864,11 +864,11 @@ private RestResponse<Job> indexVariantSample() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantSecondarySampleIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "buildIndex",commandOptions.buildIndex, true);
-            putNestedIfNotNull(beanParams, "annotate",commandOptions.annotate, true);
-            putNestedIfNotNull(beanParams, "familyIndex",commandOptions.familyIndex, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "buildIndex", commandOptions.buildIndex, true);
+            putNestedIfNotNull(beanParams, "annotate", commandOptions.annotate, true);
+            putNestedIfNotNull(beanParams, "familyIndex", commandOptions.familyIndex, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
 
             variantSecondarySampleIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -957,12 +957,12 @@ private RestResponse<Job> indexVariantScore() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantScoreIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "scoreName",commandOptions.scoreName, true);
-            putNestedIfNotEmpty(beanParams, "cohort1",commandOptions.cohort1, true);
-            putNestedIfNotEmpty(beanParams, "cohort2",commandOptions.cohort2, true);
-            putNestedIfNotEmpty(beanParams, "input",commandOptions.input, true);
-            putNestedIfNotEmpty(beanParams, "inputColumns",commandOptions.inputColumns, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
+            putNestedIfNotEmpty(beanParams, "scoreName", commandOptions.scoreName, true);
+            putNestedIfNotEmpty(beanParams, "cohort1", commandOptions.cohort1, true);
+            putNestedIfNotEmpty(beanParams, "cohort2", commandOptions.cohort2, true);
+            putNestedIfNotEmpty(beanParams, "input", commandOptions.input, true);
+            putNestedIfNotEmpty(beanParams, "inputColumns", commandOptions.inputColumns, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
 
             variantScoreIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1002,9 +1002,9 @@ private RestResponse<Job> variantSecondaryAnnotationIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantSecondaryAnnotationIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
 
             variantSecondaryAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1043,11 +1043,11 @@ private RestResponse<Job> variantSecondarySampleIndex() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantSecondarySampleIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "buildIndex",commandOptions.buildIndex, true);
-            putNestedIfNotNull(beanParams, "annotate",commandOptions.annotate, true);
-            putNestedIfNotNull(beanParams, "familyIndex",commandOptions.familyIndex, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "buildIndex", commandOptions.buildIndex, true);
+            putNestedIfNotNull(beanParams, "annotate", commandOptions.annotate, true);
+            putNestedIfNotNull(beanParams, "familyIndex", commandOptions.familyIndex, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
 
             variantSecondarySampleIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1113,9 +1113,9 @@ private RestResponse<Job> secondaryIndexVariant() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantSecondaryAnnotationIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotNull(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotNull(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
 
             variantSecondaryAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1176,8 +1176,8 @@ private RestResponse<Job> deleteVariantStats() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStatsDeleteParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "cohort",commandOptions.cohort, true);
-            putNestedIfNotNull(beanParams, "force",commandOptions.force, true);
+            putNestedIfNotNull(beanParams, "cohort", commandOptions.cohort, true);
+            putNestedIfNotNull(beanParams, "force", commandOptions.force, true);
 
             variantStatsDeleteParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1216,12 +1216,12 @@ private RestResponse<Job> indexVariantStats() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStatsIndexParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "cohort",commandOptions.cohort, true);
-            putNestedIfNotEmpty(beanParams, "region",commandOptions.region, true);
-            putNestedIfNotNull(beanParams, "overwriteStats",commandOptions.overwriteStats, true);
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
-            putNestedIfNotNull(beanParams, "aggregated",commandOptions.aggregated, true);
-            putNestedIfNotEmpty(beanParams, "aggregationMappingFile",commandOptions.aggregationMappingFile, true);
+            putNestedIfNotNull(beanParams, "cohort", commandOptions.cohort, true);
+            putNestedIfNotEmpty(beanParams, "region", commandOptions.region, true);
+            putNestedIfNotNull(beanParams, "overwriteStats", commandOptions.overwriteStats, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
+            putNestedIfNotNull(beanParams, "aggregated", commandOptions.aggregated, true);
+            putNestedIfNotEmpty(beanParams, "aggregationMappingFile", commandOptions.aggregationMappingFile, true);
 
             variantStatsIndexParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -1260,7 +1260,7 @@ private RestResponse<Job> deleteVariantStudy() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariantStudyDeleteParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "resume",commandOptions.resume, true);
+            putNestedIfNotNull(beanParams, "resume", commandOptions.resume, true);
 
             variantStudyDeleteParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java
index d5959ab09e..68a4eb5dc0 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java
@@ -127,12 +127,12 @@ private RestResponse<Organization> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), OrganizationCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "configuration.defaultUserExpirationDate",commandOptions.configurationDefaultUserExpirationDate, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "configuration.defaultUserExpirationDate", commandOptions.configurationDefaultUserExpirationDate, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             organizationCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -163,10 +163,10 @@ private RestResponse<Note> createNotes() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), NoteCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "visibility",commandOptions.visibility, true);
-            putNestedIfNotNull(beanParams, "valueType",commandOptions.valueType, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
+            putNestedIfNotNull(beanParams, "valueType", commandOptions.valueType, true);
 
             noteCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -230,8 +230,8 @@ private RestResponse<Note> updateNotes() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), NoteUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "visibility",commandOptions.visibility, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
 
             noteUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -263,7 +263,7 @@ private RestResponse<User> userUpdateStatus() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), UserStatusUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "status",commandOptions.status, true);
+            putNestedIfNotEmpty(beanParams, "status", commandOptions.status, true);
 
             userStatusUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -295,14 +295,14 @@ private RestResponse<User> updateUser() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), OrganizationUserUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
-            putNestedIfNotNull(beanParams, "quota.diskUsage",commandOptions.quotaDiskUsage, true);
-            putNestedIfNotNull(beanParams, "quota.cpuUsage",commandOptions.quotaCpuUsage, true);
-            putNestedIfNotNull(beanParams, "quota.maxDisk",commandOptions.quotaMaxDisk, true);
-            putNestedIfNotNull(beanParams, "quota.maxCpu",commandOptions.quotaMaxCpu, true);
-            putNestedIfNotEmpty(beanParams, "account.expirationDate",commandOptions.accountExpirationDate, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);
+            putNestedIfNotNull(beanParams, "quota.diskUsage", commandOptions.quotaDiskUsage, true);
+            putNestedIfNotNull(beanParams, "quota.cpuUsage", commandOptions.quotaCpuUsage, true);
+            putNestedIfNotNull(beanParams, "quota.maxDisk", commandOptions.quotaMaxDisk, true);
+            putNestedIfNotNull(beanParams, "quota.maxCpu", commandOptions.quotaMaxCpu, true);
+            putNestedIfNotEmpty(beanParams, "account.expirationDate", commandOptions.accountExpirationDate, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             organizationUserUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -334,11 +334,11 @@ private RestResponse<OrganizationConfiguration> updateConfiguration() throws Exc
                     .readValue(new java.io.File(commandOptions.jsonFile), OrganizationConfiguration.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "defaultUserExpirationDate",commandOptions.defaultUserExpirationDate, true);
-            putNestedIfNotNull(beanParams, "optimizations.simplifyPermissions",commandOptions.optimizationsSimplifyPermissions, true);
-            putNestedIfNotEmpty(beanParams, "token.algorithm",commandOptions.tokenAlgorithm, true);
-            putNestedIfNotEmpty(beanParams, "token.secretKey",commandOptions.tokenSecretKey, true);
-            putNestedIfNotNull(beanParams, "token.expiration",commandOptions.tokenExpiration, true);
+            putNestedIfNotEmpty(beanParams, "defaultUserExpirationDate", commandOptions.defaultUserExpirationDate, true);
+            putNestedIfNotNull(beanParams, "optimizations.simplifyPermissions", commandOptions.optimizationsSimplifyPermissions, true);
+            putNestedIfNotEmpty(beanParams, "token.algorithm", commandOptions.tokenAlgorithm, true);
+            putNestedIfNotEmpty(beanParams, "token.secretKey", commandOptions.tokenSecretKey, true);
+            putNestedIfNotNull(beanParams, "token.expiration", commandOptions.tokenExpiration, true);
 
             organizationConfiguration = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -382,12 +382,12 @@ private RestResponse<Organization> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), OrganizationUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "owner",commandOptions.owner, true);
-            putNestedIfNotNull(beanParams, "admins",commandOptions.admins, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "owner", commandOptions.owner, true);
+            putNestedIfNotNull(beanParams, "admins", commandOptions.admins, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             organizationUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java
index df4a22211a..929d89e1e4 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java
@@ -104,19 +104,19 @@ private RestResponse<Project> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ProjectCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "organism.scientificName",commandOptions.organismScientificName, true);
-            putNestedIfNotEmpty(beanParams, "organism.commonName",commandOptions.organismCommonName, true);
-            putNestedIfNotEmpty(beanParams, "organism.assembly",commandOptions.organismAssembly, true);
-            putNestedIfNotEmpty(beanParams, "cellbase.url",commandOptions.cellbaseUrl, true);
-            putNestedIfNotEmpty(beanParams, "cellbase.version",commandOptions.cellbaseVersion, true);
-            putNestedIfNotEmpty(beanParams, "cellbase.dataRelease",commandOptions.cellbaseDataRelease, true);
-            putNestedIfNotEmpty(beanParams, "cellbase.apiKey",commandOptions.cellbaseApiKey, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "organism.scientificName", commandOptions.organismScientificName, true);
+            putNestedIfNotEmpty(beanParams, "organism.commonName", commandOptions.organismCommonName, true);
+            putNestedIfNotEmpty(beanParams, "organism.assembly", commandOptions.organismAssembly, true);
+            putNestedIfNotEmpty(beanParams, "cellbase.url", commandOptions.cellbaseUrl, true);
+            putNestedIfNotEmpty(beanParams, "cellbase.version", commandOptions.cellbaseVersion, true);
+            putNestedIfNotEmpty(beanParams, "cellbase.dataRelease", commandOptions.cellbaseDataRelease, true);
+            putNestedIfNotEmpty(beanParams, "cellbase.apiKey", commandOptions.cellbaseApiKey, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             projectCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -208,14 +208,14 @@ private RestResponse<Project> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ProjectUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "organism.scientificName",commandOptions.organismScientificName, true);
-            putNestedIfNotEmpty(beanParams, "organism.commonName",commandOptions.organismCommonName, true);
-            putNestedIfNotEmpty(beanParams, "organism.assembly",commandOptions.organismAssembly, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "organism.scientificName", commandOptions.organismScientificName, true);
+            putNestedIfNotEmpty(beanParams, "organism.commonName", commandOptions.organismCommonName, true);
+            putNestedIfNotEmpty(beanParams, "organism.assembly", commandOptions.organismAssembly, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             projectUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java
index 2aaf023893..c8e02456a4 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java
@@ -133,12 +133,12 @@ private RestResponse<SampleAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
-            putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
-            putNestedIfNotEmpty(beanParams, "individual",commandOptions.individual, true);
-            putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
-            putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
-            putNestedIfNotEmpty(beanParams, "cohort",commandOptions.cohort, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "sample", commandOptions.sample, true);
+            putNestedIfNotEmpty(beanParams, "individual", commandOptions.individual, true);
+            putNestedIfNotEmpty(beanParams, "family", commandOptions.family, true);
+            putNestedIfNotEmpty(beanParams, "file", commandOptions.file, true);
+            putNestedIfNotEmpty(beanParams, "cohort", commandOptions.cohort, true);
 
             sampleAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -172,7 +172,7 @@ private RestResponse<Job> loadAnnotationSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), TsvAnnotationParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "content",commandOptions.content, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
 
             tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -207,32 +207,32 @@ private RestResponse<Sample> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "individualId",commandOptions.individualId, true);
-            putNestedIfNotEmpty(beanParams, "source.id",commandOptions.sourceId, true);
-            putNestedIfNotEmpty(beanParams, "source.name",commandOptions.sourceName, true);
-            putNestedIfNotEmpty(beanParams, "source.description",commandOptions.sourceDescription, true);
-            putNestedIfNotEmpty(beanParams, "source.source",commandOptions.sourceSource, true);
-            putNestedIfNotEmpty(beanParams, "source.url",commandOptions.sourceUrl, true);
-            putNestedIfNotEmpty(beanParams, "processing.preparationMethod",commandOptions.processingPreparationMethod, true);
-            putNestedIfNotEmpty(beanParams, "processing.extractionMethod",commandOptions.processingExtractionMethod, true);
-            putNestedIfNotEmpty(beanParams, "processing.labSampleId",commandOptions.processingLabSampleId, true);
-            putNestedIfNotEmpty(beanParams, "processing.quantity",commandOptions.processingQuantity, true);
-            putNestedIfNotEmpty(beanParams, "processing.date",commandOptions.processingDate, true);
-            putNestedIfNotNull(beanParams, "processing.attributes",commandOptions.processingAttributes, true);
-            putNestedIfNotEmpty(beanParams, "collection.type",commandOptions.collectionType, true);
-            putNestedIfNotEmpty(beanParams, "collection.quantity",commandOptions.collectionQuantity, true);
-            putNestedIfNotEmpty(beanParams, "collection.method",commandOptions.collectionMethod, true);
-            putNestedIfNotEmpty(beanParams, "collection.date",commandOptions.collectionDate, true);
-            putNestedIfNotNull(beanParams, "collection.attributes",commandOptions.collectionAttributes, true);
-            putNestedIfNotNull(beanParams, "somatic",commandOptions.somatic, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "individualId", commandOptions.individualId, true);
+            putNestedIfNotEmpty(beanParams, "source.id", commandOptions.sourceId, true);
+            putNestedIfNotEmpty(beanParams, "source.name", commandOptions.sourceName, true);
+            putNestedIfNotEmpty(beanParams, "source.description", commandOptions.sourceDescription, true);
+            putNestedIfNotEmpty(beanParams, "source.source", commandOptions.sourceSource, true);
+            putNestedIfNotEmpty(beanParams, "source.url", commandOptions.sourceUrl, true);
+            putNestedIfNotEmpty(beanParams, "processing.preparationMethod", commandOptions.processingPreparationMethod, true);
+            putNestedIfNotEmpty(beanParams, "processing.extractionMethod", commandOptions.processingExtractionMethod, true);
+            putNestedIfNotEmpty(beanParams, "processing.labSampleId", commandOptions.processingLabSampleId, true);
+            putNestedIfNotEmpty(beanParams, "processing.quantity", commandOptions.processingQuantity, true);
+            putNestedIfNotEmpty(beanParams, "processing.date", commandOptions.processingDate, true);
+            putNestedMapIfNotEmpty(beanParams, "processing.attributes", commandOptions.processingAttributes, true);
+            putNestedIfNotEmpty(beanParams, "collection.type", commandOptions.collectionType, true);
+            putNestedIfNotEmpty(beanParams, "collection.quantity", commandOptions.collectionQuantity, true);
+            putNestedIfNotEmpty(beanParams, "collection.method", commandOptions.collectionMethod, true);
+            putNestedIfNotEmpty(beanParams, "collection.date", commandOptions.collectionDate, true);
+            putNestedMapIfNotEmpty(beanParams, "collection.attributes", commandOptions.collectionAttributes, true);
+            putNestedIfNotNull(beanParams, "somatic", commandOptions.somatic, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             sampleCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -444,33 +444,33 @@ private RestResponse<Sample> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), SampleUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "individualId",commandOptions.individualId, true);
-            putNestedIfNotEmpty(beanParams, "source.id",commandOptions.sourceId, true);
-            putNestedIfNotEmpty(beanParams, "source.name",commandOptions.sourceName, true);
-            putNestedIfNotEmpty(beanParams, "source.description",commandOptions.sourceDescription, true);
-            putNestedIfNotEmpty(beanParams, "source.source",commandOptions.sourceSource, true);
-            putNestedIfNotEmpty(beanParams, "source.url",commandOptions.sourceUrl, true);
-            putNestedIfNotEmpty(beanParams, "processing.preparationMethod",commandOptions.processingPreparationMethod, true);
-            putNestedIfNotEmpty(beanParams, "processing.extractionMethod",commandOptions.processingExtractionMethod, true);
-            putNestedIfNotEmpty(beanParams, "processing.labSampleId",commandOptions.processingLabSampleId, true);
-            putNestedIfNotEmpty(beanParams, "processing.quantity",commandOptions.processingQuantity, true);
-            putNestedIfNotEmpty(beanParams, "processing.date",commandOptions.processingDate, true);
-            putNestedIfNotNull(beanParams, "processing.attributes",commandOptions.processingAttributes, true);
-            putNestedIfNotEmpty(beanParams, "collection.type",commandOptions.collectionType, true);
-            putNestedIfNotEmpty(beanParams, "collection.quantity",commandOptions.collectionQuantity, true);
-            putNestedIfNotEmpty(beanParams, "collection.method",commandOptions.collectionMethod, true);
-            putNestedIfNotEmpty(beanParams, "collection.date",commandOptions.collectionDate, true);
-            putNestedIfNotNull(beanParams, "collection.attributes",commandOptions.collectionAttributes, true);
-            putNestedIfNotNull(beanParams, "qualityControl.files",commandOptions.qualityControlFiles, true);
-            putNestedIfNotNull(beanParams, "somatic",commandOptions.somatic, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "individualId", commandOptions.individualId, true);
+            putNestedIfNotEmpty(beanParams, "source.id", commandOptions.sourceId, true);
+            putNestedIfNotEmpty(beanParams, "source.name", commandOptions.sourceName, true);
+            putNestedIfNotEmpty(beanParams, "source.description", commandOptions.sourceDescription, true);
+            putNestedIfNotEmpty(beanParams, "source.source", commandOptions.sourceSource, true);
+            putNestedIfNotEmpty(beanParams, "source.url", commandOptions.sourceUrl, true);
+            putNestedIfNotEmpty(beanParams, "processing.preparationMethod", commandOptions.processingPreparationMethod, true);
+            putNestedIfNotEmpty(beanParams, "processing.extractionMethod", commandOptions.processingExtractionMethod, true);
+            putNestedIfNotEmpty(beanParams, "processing.labSampleId", commandOptions.processingLabSampleId, true);
+            putNestedIfNotEmpty(beanParams, "processing.quantity", commandOptions.processingQuantity, true);
+            putNestedIfNotEmpty(beanParams, "processing.date", commandOptions.processingDate, true);
+            putNestedMapIfNotEmpty(beanParams, "processing.attributes", commandOptions.processingAttributes, true);
+            putNestedIfNotEmpty(beanParams, "collection.type", commandOptions.collectionType, true);
+            putNestedIfNotEmpty(beanParams, "collection.quantity", commandOptions.collectionQuantity, true);
+            putNestedIfNotEmpty(beanParams, "collection.method", commandOptions.collectionMethod, true);
+            putNestedIfNotEmpty(beanParams, "collection.date", commandOptions.collectionDate, true);
+            putNestedMapIfNotEmpty(beanParams, "collection.attributes", commandOptions.collectionAttributes, true);
+            putNestedIfNotNull(beanParams, "qualityControl.files", commandOptions.qualityControlFiles, true);
+            putNestedIfNotNull(beanParams, "somatic", commandOptions.somatic, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
 
             sampleUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java
index e2e2180f4d..0c18639ed5 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java
@@ -178,9 +178,9 @@ private RestResponse<StudyAclEntryList> updateAcl() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), StudyAclUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "study",commandOptions.study, true);
-            putNestedIfNotEmpty(beanParams, "template",commandOptions.template, true);
-            putNestedIfNotEmpty(beanParams, "permissions",commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "study", commandOptions.study, true);
+            putNestedIfNotEmpty(beanParams, "template", commandOptions.template, true);
+            putNestedIfNotEmpty(beanParams, "permissions", commandOptions.permissions, true);
 
             studyAclUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -212,18 +212,18 @@ private RestResponse<Study> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), StudyCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "alias",commandOptions.alias, true);
-            putNestedIfNotEmpty(beanParams, "type.id",commandOptions.typeId, true);
-            putNestedIfNotEmpty(beanParams, "type.description",commandOptions.typeDescription, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "alias", commandOptions.alias, true);
+            putNestedIfNotEmpty(beanParams, "type.id", commandOptions.typeId, true);
+            putNestedIfNotEmpty(beanParams, "type.description", commandOptions.typeDescription, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             studyCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -336,8 +336,8 @@ private RestResponse<Group> updateGroups() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), GroupCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotNull(beanParams, "users",commandOptions.users, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotNull(beanParams, "users", commandOptions.users, true);
 
             groupCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -366,7 +366,7 @@ private RestResponse<Group> updateGroupsUsers() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), GroupUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "users",commandOptions.users, true);
+            putNestedIfNotNull(beanParams, "users", commandOptions.users, true);
 
             groupUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -397,10 +397,10 @@ private RestResponse<Note> createNotes() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), NoteCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "visibility",commandOptions.visibility, true);
-            putNestedIfNotNull(beanParams, "valueType",commandOptions.valueType, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
+            putNestedIfNotNull(beanParams, "valueType", commandOptions.valueType, true);
 
             noteCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -463,8 +463,8 @@ private RestResponse<Note> updateNotes() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), NoteUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotNull(beanParams, "tags",commandOptions.tags, true);
-            putNestedIfNotNull(beanParams, "visibility",commandOptions.visibility, true);
+            putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
 
             noteUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -500,10 +500,10 @@ private RestResponse<PermissionRule> updatePermissionRules() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PermissionRule.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotNull(beanParams, "query",commandOptions.query, true);
-            putNestedIfNotNull(beanParams, "members",commandOptions.members, true);
-            putNestedIfNotNull(beanParams, "permissions",commandOptions.permissions, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedMapIfNotEmpty(beanParams, "query", commandOptions.query, true);
+            putNestedIfNotNull(beanParams, "members", commandOptions.members, true);
+            putNestedIfNotNull(beanParams, "permissions", commandOptions.permissions, true);
 
             permissionRule = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -578,17 +578,17 @@ private RestResponse<Study> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), StudyUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "alias",commandOptions.alias, true);
-            putNestedIfNotEmpty(beanParams, "type.id",commandOptions.typeId, true);
-            putNestedIfNotEmpty(beanParams, "type.description",commandOptions.typeDescription, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotEmpty(beanParams, "creationDate",commandOptions.creationDate, true);
-            putNestedIfNotEmpty(beanParams, "modificationDate",commandOptions.modificationDate, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
-            putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);
-            putNestedIfNotEmpty(beanParams, "status.name",commandOptions.statusName, true);
-            putNestedIfNotEmpty(beanParams, "status.description",commandOptions.statusDescription, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "alias", commandOptions.alias, true);
+            putNestedIfNotEmpty(beanParams, "type.id", commandOptions.typeId, true);
+            putNestedIfNotEmpty(beanParams, "type.description", commandOptions.typeDescription, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
+            putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
+            putNestedIfNotEmpty(beanParams, "status.name", commandOptions.statusName, true);
+            putNestedIfNotEmpty(beanParams, "status.description", commandOptions.statusDescription, true);
 
             studyUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -628,11 +628,11 @@ private RestResponse<VariableSet> updateVariableSets() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), VariableSetCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotNull(beanParams, "unique",commandOptions.unique, true);
-            putNestedIfNotNull(beanParams, "confidential",commandOptions.confidential, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotNull(beanParams, "unique", commandOptions.unique, true);
+            putNestedIfNotNull(beanParams, "confidential", commandOptions.confidential, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
 
             variableSetCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -661,18 +661,18 @@ private RestResponse<VariableSet> updateVariableSetsVariables() throws Exception
                     .readValue(new java.io.File(commandOptions.jsonFile), Variable.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "category",commandOptions.category, true);
-            putNestedIfNotNull(beanParams, "type",commandOptions.type, true);
-            putNestedIfNotNull(beanParams, "required",commandOptions.required, true);
-            putNestedIfNotNull(beanParams, "multiValue",commandOptions.multiValue, true);
-            putNestedIfNotNull(beanParams, "allowedValues",commandOptions.allowedValues, true);
-            putNestedIfNotNull(beanParams, "allowedKeys",commandOptions.allowedKeys, true);
-            putNestedIfNotNull(beanParams, "rank",commandOptions.rank, true);
-            putNestedIfNotEmpty(beanParams, "dependsOn",commandOptions.dependsOn, true);
-            putNestedIfNotEmpty(beanParams, "description",commandOptions.description, true);
-            putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "category", commandOptions.category, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
+            putNestedIfNotNull(beanParams, "required", commandOptions.required, true);
+            putNestedIfNotNull(beanParams, "multiValue", commandOptions.multiValue, true);
+            putNestedIfNotNull(beanParams, "allowedValues", commandOptions.allowedValues, true);
+            putNestedIfNotNull(beanParams, "allowedKeys", commandOptions.allowedKeys, true);
+            putNestedIfNotNull(beanParams, "rank", commandOptions.rank, true);
+            putNestedIfNotEmpty(beanParams, "dependsOn", commandOptions.dependsOn, true);
+            putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
+            putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
 
             variable = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java
index 4883cedef5..5f8dfce148 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java
@@ -136,11 +136,11 @@ private RestResponse<User> create() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), UserCreateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
-            putNestedIfNotEmpty(beanParams, "password",commandOptions.password, true);
-            putNestedIfNotEmpty(beanParams, "organization",commandOptions.organization, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);
+            putNestedIfNotEmpty(beanParams, "password", commandOptions.password, true);
+            putNestedIfNotEmpty(beanParams, "organization", commandOptions.organization, true);
 
             userCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -178,11 +178,11 @@ private RestResponse<User> password() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), PasswordChangeParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "organizationId",commandOptions.organizationId, true);
-            putNestedIfNotEmpty(beanParams, "user",commandOptions.user, true);
-            putNestedIfNotEmpty(beanParams, "password",commandOptions.password, true);
-            putNestedIfNotEmpty(beanParams, "newPassword",commandOptions.newPassword, true);
-            putNestedIfNotEmpty(beanParams, "reset",commandOptions.reset, true);
+            putNestedIfNotEmpty(beanParams, "organizationId", commandOptions.organizationId, true);
+            putNestedIfNotEmpty(beanParams, "user", commandOptions.user, true);
+            putNestedIfNotEmpty(beanParams, "password", commandOptions.password, true);
+            putNestedIfNotEmpty(beanParams, "newPassword", commandOptions.newPassword, true);
+            putNestedIfNotEmpty(beanParams, "reset", commandOptions.reset, true);
 
             passwordChangeParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -253,8 +253,8 @@ private RestResponse<ObjectMap> updateConfigs() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), ConfigUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "id",commandOptions.id, true);
-            putNestedIfNotNull(beanParams, "configuration",commandOptions.configuration, true);
+            putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedMapIfNotEmpty(beanParams, "configuration", commandOptions.configuration, true);
 
             configUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
@@ -303,8 +303,8 @@ private RestResponse<User> update() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), UserUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true);
-            putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true);
+            putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
+            putNestedIfNotEmpty(beanParams, "email", commandOptions.email, true);
 
             userUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java
index 8befc2876c..faa3dd8626 100644
--- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java
+++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java
@@ -401,9 +401,11 @@ private String getBodyParams(RestParameter body) {
                     String javaCommandOptionsField = "commandOptions." + getJavaFieldName(restParameter);
                     String label = StringUtils.isEmpty(restParameter.getParentName()) ? restParameter.getName() : restParameter.getParentName() + "." + restParameter.getName();
                     if (restParameter.getTypeClass().equals("java.lang.String;")) {
-                        sb.append("            putNestedIfNotEmpty(beanParams, \"" + label.replaceAll("body_", "") + "\"," + javaCommandOptionsField + ", true);\n");
+                        sb.append("            putNestedIfNotEmpty(beanParams, \"" + label.replaceAll("body_", "") + "\", " + javaCommandOptionsField + ", true);\n");
+                    } else if (isValidMap(restParameter)) {
+                        sb.append("            putNestedMapIfNotEmpty(beanParams, \"" + label.replaceAll("body_", "") + "\", " + javaCommandOptionsField + ", true);\n");
                     } else {
-                        sb.append("            putNestedIfNotNull(beanParams, \"" + label.replaceAll("body_", "") + "\"," + javaCommandOptionsField + ", true);\n");
+                        sb.append("            putNestedIfNotNull(beanParams, \"" + label.replaceAll("body_", "") + "\", " + javaCommandOptionsField + ", true);\n");
                     }
                 }
             }