Mount workdir in docker container for awsbatch

modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy

@@ -128,6 +128,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
                 cliPath: executor.getSession().getExecConfigProp(name,'awscli',null) as String,
                 storageClass: executor.getSession().config.navigate('aws.client.uploadStorageClass') as String,
                 storageEncryption: executor.getSession().config.navigate('aws.client.storageEncryption') as String,
+                mountPoint: executor.getSession().config.navigate('aws.mountPoint', '/tmp') as String,
                 remoteBinDir: executor.remoteBinDir as String,
                 region: executor.getSession().config.navigate('aws.region') as String
         )
@@ -376,29 +377,49 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         result.setJobDefinitionName(name)
         result.setType(JobDefinitionType.Container)
 
+        def mountPointPath = getAwsOptions().mountPoint
+
         // container definition
         def container = new ContainerProperties()
                 .withImage(image)
         // note the actual command, memory and cpus are overridden when the job is executed
                 .withCommand('true')
                 .withMemory(1024)
                 .withVcpus(1)
+
         def awscli = getAwsOptions().cliPath
+        def mounts = new LinkedList<MountPoint>()
+        def volumes = new LinkedList<Volume>()
+        def mountPointName = 'mount'
+        def mountWorkDir = new MountPoint()
+                    .withSourceVolume(mountPointName)
+                    .withContainerPath(mountPointPath)
+                    .withReadOnly(false)
+        mounts.add(mountWorkDir)
+        def volumeWorkDir = new Volume()
+                .withName(mountPointName)
+                .withHost(new Host()
+                .withSourcePath(mountPointPath))
+        volumes.add(volumeWorkDir)
+
         if( awscli ) {
             def mountName = 'aws-cli'
             def path = Paths.get(awscli).parent.parent.toString()
             def mount = new MountPoint()
                     .withSourceVolume(mountName)
                     .withContainerPath(path)
                     .withReadOnly(true)
-            container.setMountPoints([mount])
+            mounts.add(mount)
 
             def vol = new Volume()
                     .withName(mountName)
                     .withHost(new Host()
                     .withSourcePath(path))
-            container.setVolumes([vol])
+            volumes.add(vol)
         }
+        container.setMountPoints(mounts)
+        container.setVolumes(volumes)
+
         result.setContainerProperties(container)
 
         // create a job marker uuid

modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsOptions.groovy

@@ -42,6 +42,8 @@ class AwsOptions {
 
     String region
 
+    String mountPoint
+
     AwsOptions() { }
 
     AwsOptions(Session session) {
@@ -78,6 +80,15 @@ class AwsOptions {
         }
     }
 
+    void setMountPath(String value) {
+        if( !value )
+            this.mountPoint = '/tmp'
+        else {
+            if (!value.startsWith('/')) throw new ProcessUnrecoverableException("Not a valid mount path: $value -- it must be an absolute path")
+            this.mountPoint = value
+        }
+    }
+
     String getAwsCli() {
         def result = getCliPath()
         if( !result ) result = 'aws'

modules/nextflow/src/test/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy

@@ -457,25 +457,35 @@ class AwsBatchTaskHandlerTest extends Specification {
         def result = handler.makeJobDefRequest(IMAGE)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
-        1 * handler.getAwsOptions() >> new AwsOptions()
+        2 * handler.getAwsOptions() >> new AwsOptions()
         result.jobDefinitionName == JOB_NAME
         result.type == 'container'
         result.parameters.'nf-token' == 'fdb5ef295f566138a43252b2ea272282'
-        !result.containerProperties.mountPoints
+        result.containerProperties.mountPoints[0].sourceVolume == 'mount'
+        !result.containerProperties.mountPoints[0].readOnly
 
         when:
         result = handler.makeJobDefRequest(IMAGE)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
-        1 * handler.getAwsOptions() >> new AwsOptions(cliPath: '/home/conda/bin/aws')
+        2 * handler.getAwsOptions() >> new AwsOptions(cliPath: '/home/conda/bin/aws', mountPoint: '/tmp')
         result.jobDefinitionName == JOB_NAME
         result.type == 'container'
         result.parameters.'nf-token' == '9c56fd073d32e0c29f51f12afdfe4750'
-        result.containerProperties.mountPoints[0].sourceVolume == 'aws-cli'
-        result.containerProperties.mountPoints[0].containerPath == '/home/conda'
-        result.containerProperties.mountPoints[0].readOnly
-        result.containerProperties.volumes[0].host.sourcePath == '/home/conda'
-        result.containerProperties.volumes[0].name == 'aws-cli'
+        result.containerProperties.mountPoints[0].sourceVolume == 'mount'
+        result.containerProperties.mountPoints[0].containerPath == '/tmp'
+        !result.containerProperties.mountPoints[0].readOnly
+        result.containerProperties.volumes[0].host.sourcePath == '/tmp'
+        result.containerProperties.volumes[0].name == 'mount'
+
+        result.containerProperties.mountPoints[1].sourceVolume == 'aws-cli'
+        result.containerProperties.mountPoints[1].containerPath == '/home/conda'
+        result.containerProperties.mountPoints[1].readOnly
+        result.containerProperties.volumes[1].host.sourcePath == '/home/conda'
+        result.containerProperties.volumes[1].name == 'aws-cli'
+
+        result.containerProperties.environment[0].name == "TMPDIR"
+        result.containerProperties.environment[0].value == "/tmp"
 
     }