Fix: tolerate spaces in $NXF_TASK_WORKDIR

Prior to this commit, selecting a workDir with spaces or other special
Bash characters in the pathname — like `(`, `)`, etc — would result in
`cd $NXF_TASK_WORKDIR` failing. Now `$NXF_TASK_WORKDIR` is correctly
quoted in the generated `.output.run` scripts.

Signed-off-by: Brooks J Rady <[email protected]>

Author: TheLostLambda

modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy

@@ -229,7 +229,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
         if( launcher ) {
             def result = getRunCommand()
-            result += entryPoint ? " $entryPoint -c \"cd \$NXF_TASK_WORKDIR; $launcher\"" : " $launcher"
+            result += entryPoint ? " $entryPoint -c \"cd \\\"\$NXF_TASK_WORKDIR\\\"; $launcher\"" : " $launcher"
             return result
         }
         return getRunCommand() + ' ' + launcher

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -608,7 +608,7 @@ class BashWrapperBuilder {
             final needChangeTaskWorkDir = containerBuilder instanceof SingularityBuilder
             if( (env || needChangeTaskWorkDir) && !containerConfig.entrypointOverride() ) {
                 if( needChangeTaskWorkDir )
-                    cmd = 'cd $NXF_TASK_WORKDIR; ' + cmd
+                    cmd = 'cd \\"$NXF_TASK_WORKDIR\\"; ' + cmd
                 cmd = "/bin/bash -c \"$cmd\""
             }
             launcher = containerBuilder.getRunCommand(cmd)

modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy

@@ -217,7 +217,7 @@ class ApptainerBuilderTest extends Specification {
         when:
         cmd = new ApptainerBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd $NXF_TASK_WORKDIR; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd \\"$NXF_TASK_WORKDIR\\"; bwa --this --that file.fastq"'
     }
 
     @Unroll

modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy

@@ -218,7 +218,7 @@ class SingularityBuilderTest extends Specification {
         when:
         cmd = new SingularityBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd $NXF_TASK_WORKDIR; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd \\"$NXF_TASK_WORKDIR\\"; bwa --this --that file.fastq"'
     }
 
     @Unroll

modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy

@@ -1126,7 +1126,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: new SingularityConfig(enabled: true) ).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 $NXF_TASK_WORKDIR; 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"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd \\"$NXF_TASK_WORKDIR\\"; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1140,7 +1140,7 @@ class BashWrapperBuilderTest extends Specification {
             containerConfig: new SingularityConfig(enabled: true) ).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 $NXF_TASK_WORKDIR; /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$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 \\"$NXF_TASK_WORKDIR\\"; /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1154,7 +1154,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: new SingularityConfig(enabled: true, entrypointOverride: true) ).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 $NXF_TASK_WORKDIR; 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"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd \\"$NXF_TASK_WORKDIR\\"; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1168,7 +1168,7 @@ class BashWrapperBuilderTest extends Specification {
             containerConfig: new SingularityConfig(enabled: true, ociMode: true) ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --oci -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $NXF_TASK_WORKDIR; 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"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --oci -B /work/dir docker://ubuntu:latest /bin/bash -c "cd \\"$NXF_TASK_WORKDIR\\"; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }