Fix -with-apptainer cli option (#3621)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
nextflow-io · Feb 8, 2023 · 8c9588f · 8c9588f
1 parent 12782ee
commit 8c9588f
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diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -743,6 +743,10 @@ class ConfigBuilder {
             configContainer(config, 'singularity', cmdRun.withSingularity)
         }
 
+        if( cmdRun.withApptainer ) {
+            configContainer(config, 'apptainer', cmdRun.withApptainer)
+        }
+
         if( cmdRun.withCharliecloud ) {
             configContainer(config, 'charliecloud', cmdRun.withCharliecloud)
         }

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy
@@ -494,6 +494,7 @@ class K8sDriverLauncher {
                 cmd.&executorOptions,
                 cmd.&stdin,
                 cmd.&withSingularity,
+                cmd.&withApptainer,
                 cmd.&withDocker,
                 cmd.&withoutDocker,
                 cmd.&withMpi,