accept local singularity images

weng-lab · Oct 22, 2023 · d6d11b8 · d6d11b8
1 parent f7ec832
commit d6d11b8
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -13,7 +13,7 @@ plugins {
 }
 
 group = "io.krews"
-version = "0.14.14"
+version = "0.14.15"
 
 repositories {
     maven { setUrl("https://dl.bintray.com/kotlin/kotlin-eap") }

diff --git a/src/main/kotlin/krews/executor/bsub/BsubExecutor.kt b/src/main/kotlin/krews/executor/bsub/BsubExecutor.kt
@@ -191,9 +191,10 @@ class BsubExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirected
             bsubScript.append("export SINGULARITY_BIND=\"$binds\"\n")
 
             // Add running the task to script
+            val remoteImage = !taskRunContext.dockerImage.endsWith(".sif")
             bsubScript.append("\n")
             bsubScript.append("# Run task command.\n")
-            bsubScript.append("singularity exec --containall docker://${taskRunContext.dockerImage} $containerCommand")
+            bsubScript.append("singularity exec --containall ${if (remoteImage) "docker://" else ""}${taskRunContext.dockerImage} $containerCommand")
             bsubScript.append("\n")
 
             // Add copying output files into output dir to script