From 3f4f00f98153e89b152ee5d6fd4df7a7b5af2cfe Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 22 Apr 2022 00:00:45 +0200
Subject: [PATCH] Add support for container options to Azure Batch

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/nextflow/cloud/azure/batch/AzBatchService.groovy   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

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 e56175b046..ba8af493f8 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
@@ -349,10 +349,14 @@ class AzBatchService implements Closeable {
         config.storage().getFileShares().each {
             volumes += " -v ${mountPath}/${it.key}:${it.value.mountPath}:rw"
         }
+        // container settings
+        def opts = "-v /etc/ssl/certs:/etc/ssl/certs:ro -v /etc/pki:/etc/pki:ro ${volumes} "
+        if( task.config.getContainerOptions() )
+            opts += "${task.config.getContainerOptions()} "
         final containerOpts = new TaskContainerSettings()
                 .withImageName(container)
                 // mount host certificates otherwise `azcopy` fails
-                .withContainerRunOptions("-v /etc/ssl/certs:/etc/ssl/certs:ro -v /etc/pki:/etc/pki:ro ${volumes} ")
+                .withContainerRunOptions(opts)
 
         final slots = computeSlots(task, pool)
         log.trace "[AZURE BATCH] Submitting task: $taskId, cpus=${task.config.getCpus()}, mem=${task.config.getMemory()?:'-'}, slots: $slots"