Fix Change work dir for Singularity [ci fast]

Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Nov 6, 2023 · dbbc8e6 · dbbc8e6
1 parent 77bd6a4
commit dbbc8e6
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Showing 2 changed files with 20 additions and 2 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -480,8 +480,12 @@ class BashWrapperBuilder {
          */
         if( containerBuilder ) {
             String cmd = env ? 'eval $(nxf_container_env); ' + launcher : launcher
-            if( env && !containerConfig.entrypointOverride() ) {
-                if( containerBuilder instanceof SingularityBuilder )
+            // wrap the command with an extra bash invocation either :
+            // - to propagate the container environment or
+            // - to change in the task work directory as required by singularity
+            final needChangeTaskWorkDir = containerBuilder instanceof SingularityBuilder
+            if( (env || needChangeTaskWorkDir) && !containerConfig.entrypointOverride() ) {
+                if( needChangeTaskWorkDir )
                     cmd = 'cd $PWD; ' + cmd
                 cmd = "/bin/bash -c \"$cmd\""
             }

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -996,6 +996,20 @@ class BashWrapperBuilderTest extends Specification {
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
+    def 'should create wrapper with singularity and no env'() {
+        when:
+        def binding = newBashWrapperBuilder(
+            containerEnabled: true,
+            containerImage: 'docker://ubuntu:latest',
+            environment: [:],
+            containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
+
+        then:
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; /bin/bash -ue /work/dir/.command.sh"'
+        binding.cleanup_cmd == ""
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
+    }
+
     def 'should create wrapper with singularity legacy entry'() {
         when:
         def binding = newBashWrapperBuilder(