From 21a82aa5ae4039d7323f82c594d31ebbbdc5878f Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 8 Nov 2024 16:55:08 +0000
Subject: [PATCH 01/10] Make the container directive optional when using Azure
 Batch

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../main/nextflow/cloud/azure/batch/AzBatchService.groovy  | 7 +++++--
 .../nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy   | 7 -------
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index cd3e4b37f5..e757db2ccd 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -393,7 +393,7 @@ class AzBatchService implements Closeable {
 
         final container = task.getContainer()
         if( !container )
-            throw new IllegalArgumentException("Missing container image for process: $task.name")
+            log.warn "Missing container image for process: $task.name"
         final taskId = "nf-${task.hash.toString()}"
         // get the pool config
         final pool = getPoolSpec(poolId)
@@ -419,8 +419,11 @@ class AzBatchService implements Closeable {
             }
         }
         // config overall container settings
-        final containerOpts = new BatchTaskContainerSettings(container)
+        BatchTaskContainerSettings containerOpts = null
+        if (container) {
+            containerOpts = new BatchTaskContainerSettings(container)
                 .setContainerRunOptions(opts)
+        }
         // submit command line
         final String cmd = fusionEnabled
                 ? launcher.fusionSubmitCli(task).join(' ')
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
index 581bed4ec7..50832f2129 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
@@ -60,7 +60,6 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         this.outputFile = task.workDir.resolve(TaskRun.CMD_OUTFILE)
         this.errorFile = task.workDir.resolve(TaskRun.CMD_ERRFILE)
         this.exitFile = task.workDir.resolve(TaskRun.CMD_EXIT)
-        validateConfiguration()
     }
 
     /** only for testing purpose - DO NOT USE */
@@ -70,12 +69,6 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return executor.batchService
     }
 
-    void validateConfiguration() {
-        if (!task.container) {
-            throw new ProcessUnrecoverableException("No container image specified for process $task.name -- Either specify the container to use in the process definition or with 'process.container' value in your config")
-        }
-    }
-
     protected BashWrapperBuilder createBashWrapper() {
         fusionEnabled()
                 ? fusionLauncher()

From 8fca02a5fb0b97f9b83bbee84a6d408c5bb3ea5c Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 8 Nov 2024 17:14:30 +0000
Subject: [PATCH 02/10] Remove null container from task spec to make cleaner
 report in Azure Batch

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../nextflow/cloud/azure/batch/AzBatchService.groovy     | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index e757db2ccd..e8f6415a59 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -437,15 +437,18 @@ class AzBatchService implements Closeable {
 
         log.trace "[AZURE BATCH] Submitting task: $taskId, cpus=${task.config.getCpus()}, mem=${task.config.getMemory()?:'-'}, slots: $slots"
 
-        return new BatchTaskCreateContent(taskId, cmd)
+        final batchTask = new BatchTaskCreateContent(taskId, cmd)
                 .setUserIdentity(userIdentity(pool.opts.privileged, pool.opts.runAs, AutoUserScope.TASK))
-                .setContainerSettings(containerOpts)
                 .setResourceFiles(resourceFileUrls(task, sas))
                 .setOutputFiles(outputFileUrls(task, sas))
                 .setRequiredSlots(slots)
                 .setConstraints(constraints)
-                
 
+        if (containerOpts) {
+            batchTask.setContainerSettings(containerOpts)
+        }
+
+        return batchTask
     }
 
     AzTaskKey runTask(String poolId, String jobId, TaskRun task) {

From 3a1cbaf68533c1b31ab53202be48896ac92957f7 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 22 Nov 2024 17:51:02 +0000
Subject: [PATCH 03/10] update azure batch tests

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../azure/batch/AzBatchServiceTest.groovy     | 76 +++++++++++++++++++
 .../azure/batch/AzBatchTaskHandlerTest.groovy |  8 +-
 2 files changed, 79 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
index eceeb644b2..35897374f4 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
@@ -739,4 +739,80 @@ class AzBatchServiceTest extends Specification {
         [managedIdentity: [clientId: 'client-123']]     | 'client-123'
     }
 
+    def 'should create task for submit without container' () {
+        given:
+        Global.session = Mock(Session) { getConfig()>>[:] }
+        and:
+        def POOL_ID = 'my-pool'
+        def SAS = '123'
+        def CONFIG = [storage: [sasToken: SAS]]
+        def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
+        AzBatchService azure = Spy(new AzBatchService(exec))
+        and:
+        def TASK = Mock(TaskRun) {
+            getHash() >> HashCode.fromInt(1)
+            getContainer() >> null
+            getConfig() >> Mock(TaskConfig)
+        }
+        and:
+        def SPEC = new AzVmPoolSpec(poolId: POOL_ID, vmType: Mock(AzVmType), opts: new AzPoolOpts([:]))
+
+        when:
+        def result = azure.createTask(POOL_ID, 'salmon', TASK)
+        then:
+        1 * azure.getPoolSpec(POOL_ID) >> SPEC
+        1 * azure.computeSlots(TASK, SPEC) >> 4
+        1 * azure.resourceFileUrls(TASK, SAS) >> []
+        1 * azure.outputFileUrls(TASK, SAS) >> []
+        and:
+        result.id == 'nf-01000000'
+        result.requiredSlots == 4
+        and:
+        result.commandLine == "sh -c 'bash .command.run 2>&1 | tee .command.log'"
+        and:
+        result.containerSettings == null
+    }
+
+    def 'should create task for submit with container and fusion' () {
+        given:
+        def SAS = '1234567890' * 10
+        def AZURE = [storage: [sasToken: SAS, accountName: 'my-account']]
+        Global.session = Mock(Session) { getConfig()>>[fusion:[enabled:true], azure: AZURE] }
+        def WORKDIR = FileSystemPathFactory.parse('az://foo/work/dir')
+        and:
+        def POOL_ID = 'my-pool'
+        def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(AZURE) }
+        AzBatchService azure = Spy(new AzBatchService(exec))
+        and:
+        def TASK = Mock(TaskRun) {
+            getHash() >> HashCode.fromInt(1)
+            getContainer() >> 'ubuntu:latest'
+            getConfig() >> Mock(TaskConfig)
+            getWorkDir() >> WORKDIR
+            toTaskBean() >> Mock(TaskBean) {
+                getWorkDir() >> WORKDIR
+                getInputFiles() >> [:]
+            }
+        }
+        and:
+        def SPEC = new AzVmPoolSpec(poolId: POOL_ID, vmType: Mock(AzVmType), opts: new AzPoolOpts([:]))
+
+        when:
+        def result = azure.createTask(POOL_ID, 'salmon', TASK)
+        then:
+        1 * azure.getPoolSpec(POOL_ID) >> SPEC
+        1 * azure.computeSlots(TASK, SPEC) >> 1
+        1 * azure.resourceFileUrls(TASK, SAS) >> []
+        1 * azure.outputFileUrls(TASK, SAS) >> []
+        and:
+        result.id == 'nf-01000000'
+        result.requiredSlots == 1
+        and:
+        result.commandLine == "/usr/bin/fusion bash /fusion/az/foo/work/dir/.command.run"
+        and:
+        result.containerSettings.imageName == 'ubuntu:latest'
+        result.containerSettings.containerRunOptions.contains('--privileged')
+        result.containerSettings.containerRunOptions.contains('-e FUSION_WORK=/fusion/az/foo/work/dir')
+    }
+
 }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
index 6d0b40d4c4..fbadbc6fdd 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
@@ -18,16 +18,14 @@ import spock.lang.Specification
  */
 class AzBatchTaskHandlerTest extends Specification {
 
-    def 'should validate config' () {
+    def 'should validate config with and without container' () {
         when:
-        def task = Mock(TaskRun) { getName() >> 'foo'; }
+        def task = Mock(TaskRun) { getName() >> 'foo' }
         and:
         new AzBatchTaskHandler(task: task)
                 .validateConfiguration()
         then:
-        def e = thrown(ProcessUnrecoverableException)
-        e.message.startsWith('No container image specified for process foo')
-
+        noExceptionThrown()
 
         when:
         task = Mock(TaskRun) { getName() >> 'foo'; getContainer() >> 'ubuntu' }

From 12965bff31a743381e6bd30cec6fecb3409c7214 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 22 Nov 2024 17:55:53 +0000
Subject: [PATCH 04/10] remove test because method is removed

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../azure/batch/AzBatchTaskHandlerTest.groovy  | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
index fbadbc6fdd..4d2aa5c3e0 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
@@ -18,24 +18,6 @@ import spock.lang.Specification
  */
 class AzBatchTaskHandlerTest extends Specification {
 
-    def 'should validate config with and without container' () {
-        when:
-        def task = Mock(TaskRun) { getName() >> 'foo' }
-        and:
-        new AzBatchTaskHandler(task: task)
-                .validateConfiguration()
-        then:
-        noExceptionThrown()
-
-        when:
-        task = Mock(TaskRun) { getName() >> 'foo'; getContainer() >> 'ubuntu' }
-        and:
-        new AzBatchTaskHandler(task: task)
-                .validateConfiguration()
-        then:
-        noExceptionThrown()
-    }
-
     def 'should submit task' () {
         given:
         def builder = Mock(BashWrapperBuilder)

From ad0755584a4dce9422c5e37d767d366bc5c5eeb2 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 5 Dec 2024 16:24:35 +0000
Subject: [PATCH 05/10] Can't run gradle on the train so I'm just gonna send it

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../cloud/azure/batch/AzBatchService.groovy   |  4 +-
 .../azure/batch/AzBatchTaskHandler.groovy     |  7 ++++
 .../cloud/azure/config/AzBatchOpts.groovy     |  2 +
 .../azure/batch/AzBatchTaskHandlerTest.groovy | 39 +++++++++++++++++++
 4 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index e8f6415a59..66ae83723f 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -392,8 +392,8 @@ class AzBatchService implements Closeable {
             throw new IllegalArgumentException("Missing Azure Blob storage SAS token")
 
         final container = task.getContainer()
-        if( !container )
-            log.warn "Missing container image for process: $task.name"
+        if( !container && config.batch().requireContainer )
+            throw new IllegalArgumentException("Missing container image for process: $task.name\nYou can disable this behaviour setting `azure.batch.requireContainer=false` in the nextflow config file")
         final taskId = "nf-${task.hash.toString()}"
         // get the pool config
         final pool = getPoolSpec(poolId)
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
index 50832f2129..594577b43c 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
@@ -60,6 +60,7 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         this.outputFile = task.workDir.resolve(TaskRun.CMD_OUTFILE)
         this.errorFile = task.workDir.resolve(TaskRun.CMD_ERRFILE)
         this.exitFile = task.workDir.resolve(TaskRun.CMD_EXIT)
+        validateConfiguration()
     }
 
     /** only for testing purpose - DO NOT USE */
@@ -69,6 +70,12 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return executor.batchService
     }
 
+    void validateConfiguration() {
+        if (!task.container && config.batch().requireContainer ) {
+            throw new ProcessUnrecoverableException("No container image specified for process $task.name -- Either specify the container to use in the process definition or with 'process.container' value in your config. You can disable this behaviour setting `azure.batch.requireContainer=false` in the nextflow config file")
+        }
+    }
+
     protected BashWrapperBuilder createBashWrapper() {
         fusionEnabled()
                 ? fusionLauncher()
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
index 358c70413d..efb68b51c0 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
@@ -54,6 +54,7 @@ class AzBatchOpts implements CloudTransferOptions {
     Boolean deleteJobsOnCompletion
     Boolean deletePoolsOnCompletion
     Boolean deleteTasksOnCompletion
+    Boolean requireContainer
     CopyToolInstallMode copyToolInstallMode
 
     Map<String,AzPoolOpts> pools
@@ -67,6 +68,7 @@ class AzBatchOpts implements CloudTransferOptions {
         location = config.location
         autoPoolMode = config.autoPoolMode
         allowPoolCreation = config.allowPoolCreation
+        requireContainer = config.requireContainer ?: true
         terminateJobsOnCompletion = config.terminateJobsOnCompletion != Boolean.FALSE
         deleteJobsOnCompletion = config.deleteJobsOnCompletion
         deletePoolsOnCompletion = config.deletePoolsOnCompletion
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
index 4d2aa5c3e0..70864d7c95 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
@@ -18,6 +18,45 @@ import spock.lang.Specification
  */
 class AzBatchTaskHandlerTest extends Specification {
 
+    def 'should validate config' () {
+        when:
+        def task = Mock(TaskRun) { getName() >> 'foo'; }
+        and:
+        new AzBatchTaskHandler(task: task)
+                .validateConfiguration()
+        then:
+        def e = thrown(ProcessUnrecoverableException)
+        e.message.startsWith('No container image specified for process foo')
+
+
+        when:
+        task = Mock(TaskRun) { getName() >> 'foo'; getContainer() >> 'ubuntu' }
+        and:
+        new AzBatchTaskHandler(task: task)
+                .validateConfiguration()
+        then:
+        noExceptionThrown()
+    }
+
+    def 'should ignore missing container if disabled' () {
+        when:
+        def task = Mock(TaskRun) { getName() >> 'foo'; }
+        and:
+        new AzBatchTaskHandler(task: task, config: new AzConfig([batch: [requireContainer: false]]))
+                .validateConfiguration()
+        then:
+        noExceptionThrown()
+
+
+        when:
+        task = Mock(TaskRun) { getName() >> 'foo'; getContainer() >> 'ubuntu' }
+        and:
+        new AzBatchTaskHandler(task: task)
+                .validateConfiguration()
+        then:
+        noExceptionThrown()
+    }
+
     def 'should submit task' () {
         given:
         def builder = Mock(BashWrapperBuilder)

From 536568c30d96af8c3f802afaf20b19d38614559b Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 6 Dec 2024 12:51:59 +0000
Subject: [PATCH 06/10] Need to fixup testss

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy   | 2 +-
 .../cloud/azure/batch/AzBatchTaskHandlerTest.groovy        | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
index 594577b43c..2da2baa6bf 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
@@ -71,7 +71,7 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
     }
 
     void validateConfiguration() {
-        if (!task.container && config.batch().requireContainer ) {
+        if (!task.container && executor.config.batch().requireContainer ) {
             throw new ProcessUnrecoverableException("No container image specified for process $task.name -- Either specify the container to use in the process definition or with 'process.container' value in your config. You can disable this behaviour setting `azure.batch.requireContainer=false` in the nextflow config file")
         }
     }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
index 70864d7c95..b4988ff913 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
@@ -1,5 +1,6 @@
 package nextflow.cloud.azure.batch
 
+import nextflow.cloud.azure.config.AzConfig
 import nextflow.cloud.types.CloudMachineInfo
 import nextflow.cloud.types.PriceModel
 import nextflow.exception.ProcessUnrecoverableException
@@ -21,6 +22,9 @@ class AzBatchTaskHandlerTest extends Specification {
     def 'should validate config' () {
         when:
         def task = Mock(TaskRun) { getName() >> 'foo'; }
+        def CONFIG = [batch: [requireContainer: false]]
+        def exec = Mock(Executor) { getName() >> 'azurebatch' }
+        processor.getExecutor() >> exec
         and:
         new AzBatchTaskHandler(task: task)
                 .validateConfiguration()
@@ -41,8 +45,9 @@ class AzBatchTaskHandlerTest extends Specification {
     def 'should ignore missing container if disabled' () {
         when:
         def task = Mock(TaskRun) { getName() >> 'foo'; }
+        def CONFIG = [batch: [requireContainer: false]]
         and:
-        new AzBatchTaskHandler(task: task, config: new AzConfig([batch: [requireContainer: false]]))
+        new AzBatchTaskHandler(task: task, config: new AzConfig(CONFIG))
                 .validateConfiguration()
         then:
         noExceptionThrown()

From 762100b29ad98bfc5f10e47b6f782241d339299d Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 6 Dec 2024 13:35:12 +0000
Subject: [PATCH 07/10] fixup tests some more

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../azure/batch/AzBatchServiceTest.groovy     |  2 +-
 .../azure/batch/AzBatchTaskHandlerTest.groovy | 56 +++++++++++++------
 2 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
index 35897374f4..45b58011bb 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
@@ -745,7 +745,7 @@ class AzBatchServiceTest extends Specification {
         and:
         def POOL_ID = 'my-pool'
         def SAS = '123'
-        def CONFIG = [storage: [sasToken: SAS]]
+        def CONFIG = [storage: [sasToken: SAS], batch: [requireContainer: false]]
         def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
         AzBatchService azure = Spy(new AzBatchService(exec))
         and:
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
index b4988ff913..c57f7126e7 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
@@ -21,43 +21,63 @@ class AzBatchTaskHandlerTest extends Specification {
 
     def 'should validate config' () {
         when:
-        def task = Mock(TaskRun) { getName() >> 'foo'; }
-        def CONFIG = [batch: [requireContainer: false]]
-        def exec = Mock(Executor) { getName() >> 'azurebatch' }
-        processor.getExecutor() >> exec
+        def task = Mock(TaskRun) { 
+            getName() >> 'foo'
+            getProcessor() >> Mock(TaskProcessor) {
+                getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
+            }
+        }
+        def CONFIG = [batch: [requireContainer: true]]
         and:
-        new AzBatchTaskHandler(task: task)
-                .validateConfiguration()
+        new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
+            getConfig() >> new AzConfig(CONFIG)
+        }).validateConfiguration()
         then:
         def e = thrown(ProcessUnrecoverableException)
         e.message.startsWith('No container image specified for process foo')
 
-
         when:
-        task = Mock(TaskRun) { getName() >> 'foo'; getContainer() >> 'ubuntu' }
+        task = Mock(TaskRun) { 
+            getName() >> 'foo'
+            getContainer() >> 'ubuntu'
+        }
         and:
-        new AzBatchTaskHandler(task: task)
-                .validateConfiguration()
+        new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
+            getConfig() >> new AzConfig(CONFIG)
+        }).validateConfiguration()
         then:
         noExceptionThrown()
     }
 
     def 'should ignore missing container if disabled' () {
         when:
-        def task = Mock(TaskRun) { getName() >> 'foo'; }
-        def CONFIG = [batch: [requireContainer: false]]
+        def task = Mock(TaskRun) { 
+            getName() >> 'foo'
+            getContainer() >> null
+            getProcessor() >> Mock(TaskProcessor) {
+                getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
+            }
+        }
+        def CONFIG = [requireContainer: false]
         and:
-        new AzBatchTaskHandler(task: task, config: new AzConfig(CONFIG))
-                .validateConfiguration()
+        new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
+            getConfig() >> new AzConfig(CONFIG)
+        }).validateConfiguration()
         then:
         noExceptionThrown()
 
-
         when:
-        task = Mock(TaskRun) { getName() >> 'foo'; getContainer() >> 'ubuntu' }
+        task = Mock(TaskRun) { 
+            getName() >> 'foo'
+            getContainer() >> 'ubuntu'
+            getProcessor() >> Mock(TaskProcessor) {
+                getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
+            }
+        }
         and:
-        new AzBatchTaskHandler(task: task)
-                .validateConfiguration()
+        new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
+            getConfig() >> new AzConfig([:])
+        }).validateConfiguration()
         then:
         noExceptionThrown()
     }

From dd336aba62bffb3be33419dbe54186bf91c32277 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 6 Dec 2024 16:14:33 +0000
Subject: [PATCH 08/10] fixup tests some more

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../azure/batch/AzBatchTaskHandler.groovy     |  1 +
 .../azure/batch/AzBatchTaskHandlerTest.groovy | 43 +++++++------------
 2 files changed, 17 insertions(+), 27 deletions(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
index 2da2baa6bf..06448b9fd2 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
@@ -71,6 +71,7 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
     }
 
     void validateConfiguration() {
+        println "AZURE_BATCH_CONFIG: ${executor.config.batch()}"
         if (!task.container && executor.config.batch().requireContainer ) {
             throw new ProcessUnrecoverableException("No container image specified for process $task.name -- Either specify the container to use in the process definition or with 'process.container' value in your config. You can disable this behaviour setting `azure.batch.requireContainer=false` in the nextflow config file")
         }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
index c57f7126e7..fbecf1b8be 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchTaskHandlerTest.groovy
@@ -27,10 +27,9 @@ class AzBatchTaskHandlerTest extends Specification {
                 getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
             }
         }
-        def CONFIG = [batch: [requireContainer: true]]
         and:
         new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
-            getConfig() >> new AzConfig(CONFIG)
+            getConfig() >> new AzConfig([:])
         }).validateConfiguration()
         then:
         def e = thrown(ProcessUnrecoverableException)
@@ -41,43 +40,33 @@ class AzBatchTaskHandlerTest extends Specification {
             getName() >> 'foo'
             getContainer() >> 'ubuntu'
         }
+        def CONFIG = [batch: [requireContainer: true]]
         and:
         new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
-            getConfig() >> new AzConfig(CONFIG)
+            getConfig() >> new AzConfig(CONFIG) 
         }).validateConfiguration()
         then:
         noExceptionThrown()
     }
 
     def 'should ignore missing container if disabled' () {
-        when:
-        def task = Mock(TaskRun) { 
-            getName() >> 'foo'
-            getContainer() >> null
-            getProcessor() >> Mock(TaskProcessor) {
-                getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
-            }
+        given:
+        def task = Mock(TaskRun)
+        task.getName() >> 'batch-task'
+        task.getConfig() >> new TaskConfig()
+        task.getProcessor() >> Mock(TaskProcessor) {
+            getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
         }
-        def CONFIG = [requireContainer: false]
         and:
-        new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
-            getConfig() >> new AzConfig(CONFIG)
-        }).validateConfiguration()
-        then:
-        noExceptionThrown()
+        def handler = Spy(AzBatchTaskHandler)
+        handler.task = task
+        handler.executor = Mock(AzBatchExecutor) {
+            getConfig() >> new AzConfig([batch: [requireContainer: false]])
+        }
 
         when:
-        task = Mock(TaskRun) { 
-            getName() >> 'foo'
-            getContainer() >> 'ubuntu'
-            getProcessor() >> Mock(TaskProcessor) {
-                getExecutor() >> Mock(Executor) { getName() >> 'azurebatch' }
-            }
-        }
-        and:
-        new AzBatchTaskHandler(task: task, executor: Mock(AzBatchExecutor) {
-            getConfig() >> new AzConfig([:])
-        }).validateConfiguration()
+        handler.validateConfiguration()
+        
         then:
         noExceptionThrown()
     }

From 391dc5cfaa2eba82b7fb5a0f0c28f689db48eb29 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 9 Dec 2024 17:54:45 +0000
Subject: [PATCH 09/10] parse the config option correctly

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 .../src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
index efb68b51c0..cd11f88161 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
@@ -68,7 +68,7 @@ class AzBatchOpts implements CloudTransferOptions {
         location = config.location
         autoPoolMode = config.autoPoolMode
         allowPoolCreation = config.allowPoolCreation
-        requireContainer = config.requireContainer ?: true
+        requireContainer = config.requireContainer == null ? true : config.requireContainer
         terminateJobsOnCompletion = config.terminateJobsOnCompletion != Boolean.FALSE
         deleteJobsOnCompletion = config.deleteJobsOnCompletion
         deletePoolsOnCompletion = config.deletePoolsOnCompletion

From d88452b535b18392be937fa69c0767f00adba3b3 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 9 Dec 2024 17:58:07 +0000
Subject: [PATCH 10/10] Document the azure.batch.requireContainer config option

Signed-off-by: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
---
 docs/reference/config.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docs/reference/config.md b/docs/reference/config.md
index 0efb1ce6ae..80b39c355b 100644
--- a/docs/reference/config.md
+++ b/docs/reference/config.md
@@ -395,6 +395,11 @@ The following settings are available:
 `azure.batch.pools.<name>.vmType`
 : Specify the virtual machine type used by the pool identified with `<name>`.
 
+`azure.batch.requireContainer`
+: :::{versionadded} 25.01.0-edge
+  :::
+: Require the use of a container when running tasks (default: `true`). Note this requires an existing Azure Batch pool configured to not use a container image. Running a process without a container when the node pool requires one will raise an error on Azure Batch
+
 `azure.managedIdentity.clientId`
 : Specify the client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview). See {ref}`azure-managed-identities` for more details.