diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml
index fe7211f3a68..8b78fbd48bd 100644
--- a/opencga-app/pom.xml
+++ b/opencga-app/pom.xml
@@ -146,6 +146,13 @@
                     <include>compileR.sh</include>
                 </includes>
             </resource>
+            <resource>
+                <directory>src/main/resources</directory>
+                <includes>
+                    <include>cli-usage.yml</include>
+                </includes>
+                <targetPath>${project.basedir}/target/classes</targetPath>
+            </resource>
             <resource>
                 <directory>app/cloud/docker/compose</directory>
                 <filtering>true</filtering>
@@ -346,6 +353,7 @@
                                     <arg value="${project.basedir}/../opencga-core/target/classes/log4j2.internal.xml"/>
                                     <arg value="${project.basedir}/../opencga-storage/opencga-storage-core/target/classes/storage-configuration.yml"/>
                                     <arg value="${project.basedir}/../opencga-client/target/classes/client-configuration.yml"/>
+<!--                                    <arg value="${project.basedir}/src/main/resources/usage.yml"/>-->
                                     <arg value="${build.dir}/conf"/>
                                 </exec>
 
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliCategory.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliCategory.java
new file mode 100644
index 00000000000..e29646f79b8
--- /dev/null
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliCategory.java
@@ -0,0 +1,56 @@
+package org.opencb.opencga.app.cli.config;
+
+import java.util.Arrays;
+
+public class CliCategory {
+
+    private String name;
+    private String description;
+    private String[] options;
+
+    public CliCategory() {
+    }
+
+    public CliCategory(String name, String description, String[] options) {
+        this.name = name;
+        this.description = description;
+        this.options = options;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("Category{");
+        sb.append("name='").append(name).append('\'');
+        sb.append(", description='").append(description).append('\'');
+        sb.append(", options=").append(Arrays.toString(options));
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public CliCategory setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public CliCategory setDescription(String description) {
+        this.description = description;
+        return this;
+    }
+
+    public String[] getOptions() {
+        return options;
+    }
+
+    public CliCategory setOptions(String[] options) {
+        this.options = options;
+        return this;
+    }
+}
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliConfiguration.java
new file mode 100644
index 00000000000..99144d56fed
--- /dev/null
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliConfiguration.java
@@ -0,0 +1,75 @@
+package org.opencb.opencga.app.cli.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.UncheckedIOException;
+
+public class CliConfiguration {
+
+    /**
+     * The instance of Configuration that this Class is storing
+     */
+    private static CliConfiguration instance;
+
+    /**
+     * The instance of Usage that stores the "usage" information
+     */
+    private CliUsage cliUsage;
+
+    /**
+     * FILENAME is the file location of the configuration yml file
+     */
+    private String cliUsageFileName = "cli-usage.yml";
+
+    /**
+     * LOGGER is an instance of the Logger class so that we can do proper
+     * logging
+     */
+    private static final Logger logger = LoggerFactory.getLogger(CliConfiguration.class);
+
+    public static CliConfiguration getInstance() {
+        if (CliConfiguration.instance == null) {
+            CliConfiguration.instance = new CliConfiguration();
+        }
+        return CliConfiguration.instance;
+    }
+
+    private CliUsage loadConfiguration() throws IOException {
+        try (InputStream is = getClass().getClassLoader().getResourceAsStream(cliUsageFileName)) {
+            // Mapping the config from the YAML file to the Configuration class
+            ObjectMapper yamlObjectMapper = new ObjectMapper(new YAMLFactory());
+            return yamlObjectMapper.readValue(is, CliUsage.class);
+        }
+    }
+
+    /*
+     * We keep an instance of cliUsage for the Shell
+     */
+    public CliUsage getUsage() {
+        if (cliUsage == null) {
+            try {
+                cliUsage = loadConfiguration();
+            } catch (IOException e) {
+                throw new UncheckedIOException(e);
+            }
+        }
+        return cliUsage;
+    }
+
+    public void setUsage(CliUsage cliUsage) {
+        this.cliUsage = cliUsage;
+    }
+
+    public String getCliUsageFileName() {
+        return cliUsageFileName;
+    }
+
+    public void setCliUsageFileName(String cliUsageFileName) {
+        this.cliUsageFileName = cliUsageFileName;
+    }
+}
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliUsage.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliUsage.java
new file mode 100644
index 00000000000..406dac103a8
--- /dev/null
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliUsage.java
@@ -0,0 +1,32 @@
+package org.opencb.opencga.app.cli.config;
+
+import java.util.Arrays;
+
+public class CliUsage {
+
+    CliCategory[] categories;
+
+    public CliUsage() {
+    }
+
+    public CliUsage(CliCategory[] categories) {
+        this.categories = categories;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("Usage{");
+        sb.append("categories=").append(Arrays.toString(categories));
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public CliCategory[] getCategories() {
+        return categories;
+    }
+
+    public CliUsage setCategories(CliCategory[] categories) {
+        this.categories = categories;
+        return this;
+    }
+}
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
index 7639ed66faf..3c30b6d022e 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-10-20 OpenCB
+* Copyright 2015-2023-11-03 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
index 53be1d6dfbe..19ca44161d1 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-10-20 OpenCB
+* Copyright 2015-2023-11-03 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java
index 296b1be2d75..b49256292c6 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java
@@ -65,6 +65,8 @@ public static void main(String[] args) {
         }
     }
 
+
+
     private static void checkMode(String[] args) {
         if (ArrayUtils.contains(args, "--shell")) {
             setMode(Mode.SHELL);
@@ -130,7 +132,7 @@ public static void executeShell(String[] args) {
             }
             Shell.printShellHeaderMessage();
             // Create a shell executor instance
-            shell = new Shell(options);
+            shell = new Shell(options, new OpenCgaCompleterImpl(), new CommandProcessor());
             logger.debug("Shell created ");
             // Launch execute command to begin the execution
             shell.execute();
@@ -162,7 +164,7 @@ public static String[] parseCliParams(String[] args) {
         }
         logger.debug("CLI parsed params ::: " + CommandLineUtils.argsToString(args));
         String shortcut = CommandLineUtils.getShortcut(args);
-        args = CommandLineUtils.processShortCuts(args);
+        args = CommandLineUtils.processShortCuts(args, new OpencgaCliOptionsParser());
         if (args != null) {
             logger.debug("Process shortcut result ::: " + CommandLineUtils.argsToString(args));
         } else {
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomCliOptionsParser.java
index c0d30753a2f..68c964acd1f 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomCliOptionsParser.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomCliOptionsParser.java
@@ -7,11 +7,16 @@
 import org.opencb.opencga.app.cli.CliOptionsParser;
 import org.opencb.opencga.app.cli.GeneralCliOptions;
 import org.opencb.opencga.app.cli.admin.AdminCliOptionsParser;
+import org.opencb.opencga.app.cli.config.CliCategory;
+import org.opencb.opencga.app.cli.config.CliConfiguration;
+import org.opencb.opencga.app.cli.config.CliUsage;
 import org.opencb.opencga.app.cli.main.OpencgaMain;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.*;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 public class CustomCliOptionsParser extends CliOptionsParser {
 
@@ -67,6 +72,7 @@ public void printUsage() {
             } else {
                 PrintUtils.println(PrintUtils.getKeyValueAsFormattedString("Usage:", "       " + getPrefix() + "[-h|--help] [--shell] [--host] [--version] <command> [options]"));
             }
+
             System.err.println();
             printMainUsage();
             System.err.println();
@@ -97,6 +103,40 @@ private String getPrefix() {
         return "opencga.sh ";
     }
 
+    /**
+     * Read cli-usage.yml file to print the usage.
+     */
+    @Override
+    protected void printMainUsage() {
+        CliUsage cliUsage = CliConfiguration.getInstance().getUsage();
+        CliCategory[] categories = cliUsage.getCategories();
+        for (CliCategory cliCategory : categories) {
+            String[] options = cliCategory.getOptions();
+            PrintUtils.println(PrintUtils.format(cliCategory.getDescription(), PrintUtils.Color.GREEN));
+            for (String option : options) {
+                for (String command : jCommander.getCommands().keySet()) {
+                    if (command.equals(option)) {
+                        PrintUtils.printCommandHelpFormattedString(command, jCommander.getCommandDescription(command));
+                    }
+                }
+            }
+            System.err.println();
+        }
+        printOpencgaCommands();
+    }
+
+    private void printOpencgaCommands() {
+        Map<String, String> opencgaCommands = getOpencgaCommands();
+        if (!OpencgaMain.isShellMode()) {
+            PrintUtils.println(PrintUtils.format("Opencga options:", PrintUtils.Color.GREEN));
+        } else {
+            PrintUtils.println(PrintUtils.format("Opencga commands:", PrintUtils.Color.GREEN));
+        }
+        for (Map.Entry entry : opencgaCommands.entrySet()) {
+            PrintUtils.printCommandHelpFormattedString(entry.getKey().toString(), entry.getValue().toString());
+        }
+    }
+    /*
     @Override
     protected void printMainUsage() {
         Set<String> analysisCommands = new HashSet<>(Arrays.asList("alignments", "variant", "clinical"));
@@ -153,7 +193,7 @@ protected void printMainUsage() {
         for (Map.Entry entry : opencgaCommands.entrySet()) {
             PrintUtils.printCommandHelpFormattedString(entry.getKey().toString(), entry.getValue().toString());
         }
-    }
+    }*/
 
     private Map<String, String> getOpencgaCommands() {
         Map<String, String> h = new HashMap<>();
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/shell/Shell.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/shell/Shell.java
index 02ff4bc4321..00f8de6d68f 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/shell/Shell.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/shell/Shell.java
@@ -11,6 +11,7 @@
 import org.opencb.commons.utils.PrintUtils;
 import org.opencb.opencga.app.cli.GeneralCliOptions;
 import org.opencb.opencga.app.cli.main.OpenCgaCompleterImpl;
+import org.opencb.opencga.app.cli.main.OpencgaCliOptionsParser;
 import org.opencb.opencga.app.cli.main.OpencgaMain;
 import org.opencb.opencga.app.cli.main.executors.OpencgaCommandExecutor;
 import org.opencb.opencga.app.cli.main.processors.CommandProcessor;
@@ -36,13 +37,17 @@ public class Shell extends OpencgaCommandExecutor {
 
 
     // Create a command processor to process all the shell commands
-    private final CommandProcessor processor = new CommandProcessor();
+    private final CommandProcessor processor;
     private LineReader lineReader = null;
     private Terminal terminal = null;
     private String host = null;
 
-    public Shell(GeneralCliOptions.CommonCommandOptions options) throws CatalogAuthenticationException {
+    private Completer completer;
+
+    public Shell(GeneralCliOptions.CommonCommandOptions options, Completer completer, CommandProcessor processor) throws CatalogAuthenticationException {
         super(options);
+        this.completer=completer;
+        this.processor=processor;
         if (options.host != null) {
             host = options.host;
         }
@@ -104,7 +109,7 @@ private LineReader getTerminal() {
             reader = LineReaderBuilder.builder()
                     .terminal(terminal)
                     .highlighter(new DefaultHighlighter())
-                    .history(defaultHistory).completer(new OpenCgaCompleterImpl())
+                    .history(defaultHistory).completer(this.completer)
                     .build();
         } catch (Exception e) {
             CommandLineUtils.error("Failed to create terminal ", e);
@@ -209,7 +214,7 @@ public String[] parseParams(String[] args) throws CatalogAuthenticationException
                 return args;
             }
         }
-        return CommandLineUtils.processShortCuts(args);
+        return CommandLineUtils.processShortCuts(args, new OpencgaCliOptionsParser());
 
     }
 
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java
index 4454887584b..b0f83ec3886 100644
--- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java
+++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java
@@ -4,6 +4,7 @@
 import org.opencb.commons.utils.PrintUtils;
 import org.opencb.opencga.app.cli.main.OpencgaCliOptionsParser;
 import org.opencb.opencga.app.cli.main.OpencgaMain;
+import org.opencb.opencga.app.cli.main.custom.CustomCliOptionsParser;
 import org.opencb.opencga.core.common.GitRepositoryState;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -61,8 +62,8 @@ public static void error(String message, Exception e) {
         }
     }
 
-    public static String[] processShortCuts(String[] args) {
-        OpencgaCliOptionsParser cliOptionsParser = new OpencgaCliOptionsParser();
+    public static String[] processShortCuts(String[] args, CustomCliOptionsParser parser) {
+
         switch (getShortcut(args)) {
             case "login":
                 return LoginUtils.parseLoginCommand(args);
@@ -78,7 +79,7 @@ public static String[] processShortCuts(String[] args) {
                     }
                 }
                 try {
-                    cliOptionsParser.printUsage(args);
+                    parser.printUsage(args);
                 } catch (Exception e) {
                     // malformed command
                     return args;
diff --git a/opencga-app/src/main/resources/cli-usage.yml b/opencga-app/src/main/resources/cli-usage.yml
new file mode 100644
index 00000000000..a3451aea6a7
--- /dev/null
+++ b/opencga-app/src/main/resources/cli-usage.yml
@@ -0,0 +1,29 @@
+categories:
+  - name: catalog
+    description: "Catalog commands:"
+    options:
+      - users
+      - projects
+      - studies
+      - files
+      - jobs
+      - individuals
+      - families
+      - panels
+      - samples
+      - cohorts
+      - meta
+  - name: Analysis
+    description: "Analysis commands:"
+    options:
+      - alignments
+      - variant
+      - clinical
+  - name: Operation
+    description: "Operation commands:"
+    options:
+      - operations
+  - name: Administrator
+    description: "Administrator commands:"
+    options:
+      - admin
diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R
index e2e650759c0..21b9e768143 100644
--- a/opencga-client/src/main/R/R/Admin-methods.R
+++ b/opencga-client/src/main/R/R/Admin-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R
index 517d51dad14..8a5cd0de53b 100644
--- a/opencga-client/src/main/R/R/Alignment-methods.R
+++ b/opencga-client/src/main/R/R/Alignment-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R
index 8b679bba8af..f09553143fb 100644
--- a/opencga-client/src/main/R/R/AllGenerics.R
+++ b/opencga-client/src/main/R/R/AllGenerics.R
@@ -1,6 +1,6 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
@@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName,
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, members, templateId, study, variableSet, group, studies, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, variableSet, members, studies, group, study, templateId, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, annotationSet, files, members, folder, file, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, members, sample, annotationSet, samples, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, individual, annotationSet, individuals, members, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, members, families, family, annotationSet, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, members, cohorts, cohort, annotationSet, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, annotationSet, cohorts, cohort, members, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, interpretation, members, interpretations, clinicalAnalyses, clinicalAnalysis, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretation, members, interpretations, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################
@@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## GA4GHClient
-setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...)
+setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...)
     standardGeneric("ga4ghClient"))
 
 # ##############################################################################
diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R
index 5d26c3f4c93..0c29491814d 100644
--- a/opencga-client/src/main/R/R/Clinical-methods.R
+++ b/opencga-client/src/main/R/R/Clinical-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -58,7 +58,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, members, interpretations, clinicalAnalyses, clinicalAnalysis, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretation, members, interpretations, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R
index fb761746d4e..7b007db3835 100644
--- a/opencga-client/src/main/R/R/Cohort-methods.R
+++ b/opencga-client/src/main/R/R/Cohort-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, cohorts, cohort, annotationSet, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohorts, cohort, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R
index 2b4ec1fe2e8..3112cc1563b 100644
--- a/opencga-client/src/main/R/R/Family-methods.R
+++ b/opencga-client/src/main/R/R/Family-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, members, families, family, annotationSet, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R
index 75e2b732758..331f0509d45 100644
--- a/opencga-client/src/main/R/R/File-methods.R
+++ b/opencga-client/src/main/R/R/File-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, files, members, folder, file, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R
index e0db9d9f3ae..bcfca561b30 100644
--- a/opencga-client/src/main/R/R/GA4GH-methods.R
+++ b/opencga-client/src/main/R/R/GA4GH-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -31,7 +31,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) {
+setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/ga4gh/reads/search:
diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R
index 3e808df9e76..3e136adaaa9 100644
--- a/opencga-client/src/main/R/R/Individual-methods.R
+++ b/opencga-client/src/main/R/R/Individual-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, annotationSet, individuals, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R
index f01e5f44139..ddb4327e9a9 100644
--- a/opencga-client/src/main/R/R/Job-methods.R
+++ b/opencga-client/src/main/R/R/Job-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -40,7 +40,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) {
+setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R
index aa4f8f38aaf..666c2bc2d65 100644
--- a/opencga-client/src/main/R/R/Meta-methods.R
+++ b/opencga-client/src/main/R/R/Meta-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R
index 56206dd1df2..84e56923789 100644
--- a/opencga-client/src/main/R/R/Operation-methods.R
+++ b/opencga-client/src/main/R/R/Operation-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R
index 45b9913a4b1..c43aefd4e83 100644
--- a/opencga-client/src/main/R/R/Panel-methods.R
+++ b/opencga-client/src/main/R/R/Panel-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R
index acea3c5c36d..8c2b7a0fcb8 100644
--- a/opencga-client/src/main/R/R/Project-methods.R
+++ b/opencga-client/src/main/R/R/Project-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R
index d9f94ce2011..ee198ee3c12 100644
--- a/opencga-client/src/main/R/R/Sample-methods.R
+++ b/opencga-client/src/main/R/R/Sample-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, annotationSet, samples, endpointName, params=NULL, ...) {
+setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/samples/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R
index 9659a1d59e3..f9e528e2c91 100644
--- a/opencga-client/src/main/R/R/Study-methods.R
+++ b/opencga-client/src/main/R/R/Study-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -46,7 +46,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("studyClient", "OpencgaR", function(OpencgaR, members, templateId, study, variableSet, group, studies, endpointName, params=NULL, ...) {
+setMethod("studyClient", "OpencgaR", function(OpencgaR, variableSet, members, studies, group, study, templateId, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/studies/acl/{members}/update:
diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R
index 91cba91802d..d5b5cdfe796 100644
--- a/opencga-client/src/main/R/R/User-methods.R
+++ b/opencga-client/src/main/R/R/User-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) {
+setMethod("userClient", "OpencgaR", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/users/login:
diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R
index 3ad2940ffc6..20dcf8ed70d 100644
--- a/opencga-client/src/main/R/R/Variant-methods.R
+++ b/opencga-client/src/main/R/R/Variant-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-20
+#    Autogenerated on: 2023-11-03
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
index 4b1ffc655ed..712a7c20af5 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
index 3f34d8a1ae5..b44121e5a72 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
@@ -40,7 +40,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
index 8af49e36b9c..eb7f743ba10 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
@@ -51,7 +51,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
index 79b1257e020..ad36e64ed70 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
@@ -37,7 +37,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
index fe5f78505a9..cfa9601a978 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
@@ -35,7 +35,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
index abc8d908670..b524791ca20 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
index 10e7daa866f..97a97aaa3a2 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
@@ -43,7 +43,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
index 364a0f3fd71..624e63f5837 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
@@ -27,7 +27,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
index 0dc532fa526..3d60c1d23aa 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
index 846bc56452e..c377f59750b 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
@@ -37,7 +37,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
index 46feb9030f8..4c127e53014 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
@@ -28,7 +28,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
index f4dd61aaaf0..46e60e4ce05 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
@@ -32,7 +32,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
index 5e42759715a..abbfcda3ee1 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-10-20
+* Autogenerated on: 2023-11-03
 *
 * Manual changes to this file may cause unexpected behavior in your application.
 * Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
index 5c8e425988a..7501055226c 100644
--- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
+++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
@@ -45,7 +45,7 @@
 * WARNING: AUTOGENERATED CODE
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index 5b920d96a6e..4cae5fc0437 100644
--- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py
+++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py
@@ -2,7 +2,7 @@
 WARNING: AUTOGENERATED CODE
 
     This code was generated by a tool.
-    Autogenerated on: 2023-10-20
+    Autogenerated on: 2023-11-03
     
     Manual changes to this file may cause unexpected behavior in your application.
     Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
index be6b137a26f..1c71eecfa0b 100644
--- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
+++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
@@ -2,7 +2,7 @@
 WARNING: AUTOGENERATED CODE
 
     This code was generated by a tool.
-    Autogenerated on: 2023-10-20
+    Autogenerated on: 2023-11-03
     
     Manual changes to this file may cause unexpected behavior in your application.
     Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
index d096a751c9b..01015fe28d5 100644
--- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
+++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
@@ -2,7 +2,7 @@
 WARNING: AUTOGENERATED CODE
 
     This code was generated by a tool.
-    Autogenerated on: 2023-10-20
+    Autogenerated on: 2023-11-03
     
     Manual changes to this file may cause unexpected behavior in your application.
     Manual changes to this file will be overwritten if the code is regenerated.
diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/config/Options.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/config/Options.java
index 12e8f7d5e62..4a8d2e42646 100644
--- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/config/Options.java
+++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/config/Options.java
@@ -7,6 +7,7 @@
 public class Options {
 
     private String outputDir;
+    private String version;
 
     private List<String> ignoreTypes;
 
@@ -22,6 +23,15 @@ public Options setOutputDir(String outputDir) {
         return this;
     }
 
+    public String getVersion() {
+        return version;
+    }
+
+    public Options setVersion(String version) {
+        this.version = version;
+        return this;
+    }
+
     private String getFolderAsPackage(String inputDir) {
         String res = "";
         if (inputDir.contains("/src/main/java/")) {
diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java
index dd4717b0fee..121166bd9d2 100644
--- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java
+++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java
@@ -87,7 +87,7 @@ protected String getClassImports(String key) {
     protected String getClassHeader(String key) {
         StringBuilder sb = new StringBuilder();
         sb.append("\n");
-        sb.append("public class OpencgaCliOptionsParser extends CustomCliOptionsParser {\n");
+        sb.append("public class "+this.config.getOptions().getVersion()+"CliOptionsParser extends CustomCliOptionsParser {\n");
         sb.append("\n");
         for (RestCategory restCategory : availableCategories.values()) {
             sb.append("    private final " + getAsClassName(restCategory.getName()) + "CommandOptions " + getAsVariableName(restCategory.getName()) +
@@ -96,7 +96,7 @@ protected String getClassHeader(String key) {
         sb.append("\n");
         sb.append("    enum OutputFormat {IDS, ID_CSV, NAME_ID_MAP, ID_LIST, RAW, PRETTY_JSON, PLAIN_JSON}\n");
         sb.append("\n");
-        sb.append("    public OpencgaCliOptionsParser() {\n");
+        sb.append("    public "+this.config.getOptions().getVersion()+"CliOptionsParser() {\n");
         sb.append("\n");
         sb.append("        jCommander.setExpandAtSign(false);\n");
 
@@ -163,6 +163,6 @@ protected String getClassMethods(String key) {
 
     @Override
     protected String getClassFileName(String key) {
-        return config.getOptions().getOutputDir() + "/OpencgaCliOptionsParser.java";
+        return config.getOptions().getOutputDir() + "/"+this.config.getOptions().getVersion()+"CliOptionsParser.java";
     }
 }
diff --git a/opencga-server/src/main/resources/cli-config.yaml b/opencga-server/src/main/resources/cli-config.yaml
index 4e5c24c5e9d..b7cead15b73 100644
--- a/opencga-server/src/main/resources/cli-config.yaml
+++ b/opencga-server/src/main/resources/cli-config.yaml
@@ -1,4 +1,5 @@
 options:
+  version: Opencga
   outputDir: opencga-app/src/main/java/org/opencb/opencga/app/cli/main/
   ignoreTypes:
     - string