Fix Invalid setting of TMP var with singularity (2) #1997 [ci fast]

nextflow-io · Mar 28, 2021 · 472cfbd · 472cfbd
1 parent 23f8012
commit 472cfbd
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -738,7 +738,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" SINGULARITYENV_TMP="$TMP" SINGULARITYENV_TMPDIR="$TMPDIR" singularity exec docker:ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec docker:ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && kill $pid 2>/dev/null'