diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
index 50c396dd7c..41e82ac2a7 100644
--- a/.github/workflows/develop.yml
+++ b/.github/workflows/develop.yml
@@ -11,7 +11,7 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+      maven_opts: -P storage-hadoop,${{ vars.HADOOP_FLAVOUR }},RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl ':opencga-app' --also-make
 
   test:
     uses: ./.github/workflows/test-analysis.yml
@@ -24,7 +24,7 @@ jobs:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
-      maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
+      maven_opts: -P storage-hadoop,${{ vars.HADOOP_FLAVOUR }} -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
diff --git a/.github/workflows/manual-deploy-docker.yml b/.github/workflows/manual-deploy-docker.yml
index f4c79f4c24..801237902f 100644
--- a/.github/workflows/manual-deploy-docker.yml
+++ b/.github/workflows/manual-deploy-docker.yml
@@ -10,6 +10,11 @@ on:
         description: "The tag for the new docker."
         type: string
         required: true
+      hadoop_flavour:
+        description: "The hadoop flavour to use."
+        type: string
+        required: false
+        default: "emr6.1"
 
 jobs:
   build:
@@ -35,7 +40,7 @@ jobs:
             ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
           fi
       - name: Maven Build (skip tests)
-        run: mvn -T 2 clean install -DskipTests -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+        run: mvn -T 2 clean install -DskipTests -P storage-hadoop,${{ inputs.hadoop_flavour }},RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl ':opencga-app' --also-make
       - uses: actions/upload-artifact@v4
         with:
           name: build-folder
diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml
index faedd27beb..420eb11c31 100644
--- a/.github/workflows/pull-request-merge.yml
+++ b/.github/workflows/pull-request-merge.yml
@@ -13,7 +13,7 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+      maven_opts: -P storage-hadoop,${{ vars.HADOOP_FLAVOUR }},RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl ':opencga-app' --also-make
 
   delete-docker:
     uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 0481b386dc..0466b02035 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -10,13 +10,13 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+      maven_opts: -P storage-hadoop,${{ vars.HADOOP_FLAVOUR }},RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl ':opencga-app' --also-make
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: build
     with:
-      maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
+      maven_opts: -P storage-hadoop,${{ vars.HADOOP_FLAVOUR }} -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml
index 51888a9179..6e2a7b800e 100644
--- a/.github/workflows/task.yml
+++ b/.github/workflows/task.yml
@@ -12,7 +12,7 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+      maven_opts: -P storage-hadoop,${{ vars.TASK_HADOOP_FLAVOUR }},RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl ':opencga-app' --also-make
 
   test:
     uses: ./.github/workflows/test-analysis.yml
@@ -20,6 +20,7 @@ jobs:
     secrets: inherit
     with:
       test_profile: runShortTests
+      hadoop_flavour: ${{ vars.TASK_HADOOP_FLAVOUR }}
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
index ccb848d11e..85d43206a9 100644
--- a/.github/workflows/test-analysis.yml
+++ b/.github/workflows/test-analysis.yml
@@ -6,6 +6,10 @@ on:
       test_profile:
         type: string
         required: true
+      hadoop_flavour:
+        type: string
+        required: false
+        default: "emr6.1"
       mvn_opts:
         type: string
 
@@ -41,7 +45,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        run: mvn -T 2 clean install -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -DskipTests -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_opencga
+        run: mvn -T 2 clean install -P storage-hadoop,${{ inputs.hadoop_flavour }},${{ inputs.test_profile }} -DskipTests -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_opencga
 
   test:
     name: Execute JUnit and Jacoco tests
@@ -72,7 +76,7 @@ jobs:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
       - name: Run Junit tests
-        run: mvn -B verify surefire-report:report --fail-never -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }}
+        run: mvn -B verify surefire-report:report --fail-never -P storage-hadoop,${{ inputs.hadoop_flavour }},${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl ':opencga-app' --also-make ${{ inputs.mvn_opts }}
       - name: Publish Test Report
         uses: scacap/action-surefire-report@v1
         env:
diff --git a/pom.xml b/pom.xml
index 67881cc405..9be5166b35 100644
--- a/pom.xml
+++ b/pom.xml
@@ -281,7 +281,7 @@
             </dependency>
             <dependency>
                 <groupId>org.opencb.opencga</groupId>
-                <artifactId>opencga-storage-hadoop-deps-hdp3.1</artifactId>
+                <artifactId>opencga-storage-hadoop-deps-emr6.1</artifactId>
                 <version>${project.version}</version>
                 <classifier>shaded</classifier>
             </dependency>