Fix env output when changing task workdir

Signed-off-by: Paolo Di Tommaso <[email protected]>

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

@@ -95,6 +95,9 @@ class ShifterBuilder extends ContainerBuilder<ShifterBuilder> {
         else if( env instanceof String && env.contains('=') ) {
             result << env
         }
+        else if( env instanceof String ) {
+            result << "\${$env:+\"$env=\$$env\"}"
+        }
         else if( env ) {
             throw new IllegalArgumentException("Not a valid environment value: $env [${env.class.name}]")
         }

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

@@ -183,6 +183,7 @@ class BashWrapperBuilder {
         result.append('\n')
         result.append('# capture process environment\n')
         result.append('set +u\n')
+        result.append('cd "$NXF_TASK_WORKDIR"\n')
         for( int i=0; i<names.size(); i++) {
             final key = names[i]
             result.append "echo $key=\${$key[@]} "
@@ -582,6 +583,8 @@ class BashWrapperBuilder {
         if( this.containerCpuset )
             builder.addRunOptions(containerCpuset)
 
+        // export task work directory
+        builder.addEnv('NXF_TASK_WORKDIR')
         // export the nextflow script debug variable
         if( isTraceRequired() )
             builder.addEnv( 'NXF_DEBUG=${NXF_DEBUG:=0}')

modules/nextflow/src/main/resources/nextflow/executor/command-run.txt

@@ -147,6 +147,7 @@ nxf_main() {
     {{task_env}}
     {{secrets_env}}
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
     {{stage_cmd}}
 
     set +e

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

@@ -216,7 +216,7 @@ class BashWrapperBuilderTest extends Specification {
         def builder = bash.createContainerBuilder(null)
         then:
         builder instanceof SingularityBuilder
-        builder.env == ['FOO','BAR']
+        builder.env == ['NXF_TASK_WORKDIR', 'FOO','BAR']
         builder.workDir == Paths.get('/my/work/dir')
         builder.mounts == [ Paths.get('/my/bin') ]
 
@@ -720,7 +720,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -734,7 +734,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -755,7 +755,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -769,7 +769,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -790,7 +790,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerEnabled: true  ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'sudo docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
     }
@@ -803,7 +803,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, remove:false, kill: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == null
         binding.containsKey('kill_cmd')
@@ -817,7 +817,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true, remove:false, kill: 'SIGXXX'] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == 'docker kill -s SIGXXX $NXF_BOXID'
         binding.containsKey('kill_cmd')
@@ -832,7 +832,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -847,7 +847,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', sudo: true, enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
         binding.cleanup_cmd == '''\
                 (sudo -n true && sudo rm -rf "$NXF_SCRATCH" || rm -rf "$NXF_SCRATCH")&>/dev/null || true
@@ -864,7 +864,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
     }
@@ -879,7 +879,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -896,7 +896,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -921,7 +921,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -938,7 +938,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -961,7 +961,7 @@ class BashWrapperBuilderTest extends Specification {
             STATUS=$(shifterimg -v pull docker://ubuntu:latest | tail -n2 | head -n1 | awk \'{print $6}\')
             [[ $STATUS == "FAILURE" || -z $STATUS ]] && echo "Shifter failed to pull image \'docker://ubuntu:latest\'" >&2  && exit 1
         done
-        shifter --image docker://ubuntu:latest /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
+        ${NXF_TASK_WORKDIR:+"NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} shifter --image docker://ubuntu:latest /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -977,7 +977,7 @@ class BashWrapperBuilderTest extends Specification {
                 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"} singularity exec --no-home --pid 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"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid 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" ]] && nxf_kill $pid'
     }
@@ -991,7 +991,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity', entrypointOverride: true] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid 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"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid 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" ]] && nxf_kill $pid'
     }
@@ -1086,6 +1086,7 @@ class BashWrapperBuilderTest extends Specification {
         str == '''
             # capture process environment
             set +u
+            cd "$NXF_TASK_WORKDIR"
             echo FOO=${FOO[@]} > .command.env
             echo BAR=${BAR[@]} >> .command.env
             '''
@@ -1130,7 +1131,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1143,7 +1144,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true, entrypointOverride: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1157,7 +1158,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'rm -rf $NXF_SCRATCH || true\npodman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }

modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt

@@ -305,6 +305,7 @@ nxf_main() {
     set +u
     set -u
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
     nxf_stage
 
     set +e

modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt

@@ -122,6 +122,7 @@ nxf_main() {
     spack env activate -d /spack/env/path
     set -u
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
     nxf_stage
 
     set +e

plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt

@@ -210,6 +210,7 @@ nxf_main() {
     set +u
     set -u
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
 
     set +e
     (set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) &