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Fix: tolerate spaces in $NXF_TASK_WORKDIR #6421

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Fix: tolerate spaces in $NXF_TASK_WORKDIR #6421

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2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
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Expand Up @@ -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 \"$cmd\""
}
launcher = containerBuilder.getRunCommand(cmd)
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2 changes: 1 addition & 1 deletion modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
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Expand Up @@ -217,7 +217,7 @@ class ApptainerBuilderTest extends Specification {
when:
cmd = new ApptainerBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
then:
cmd == 'set +u; env - PATH="$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
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2 changes: 1 addition & 1 deletion modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
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Expand Up @@ -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
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8 changes: 4 additions & 4 deletions modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
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Expand Up @@ -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'
}
Expand All @@ -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'
}
Expand All @@ -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'
}
Expand All @@ -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'
}
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