Merge branch 'master' into 4920_azure_tasks_support_disk_directive

changelog.txt

@@ -1,5 +1,20 @@
 NEXTFLOW CHANGE-LOG
 ===================
+24.10.2 - 27 Nov 2024
+- Prevent NPE with null AWS Batch response [3d491934]
+- Fix overlapping conda lock file (#5540) [df66deaa]
+- Fix missing wave response (#5547) [eb85cda8]
+- Bump nf-wave@1.7.4 [93d09404]
+- Bump nf-amazon@2.9.2 [469a35dd]
+
+24.10.1 - 18 Nov 2024
+- Fix overlapping file lock exception (#5489) [a2566d54]
+- Fix isContainerReady when wave is disabled (#5509) [c69e3711]
+- Bump nf-wave@1.7.3 [e7709a0f]
+- Bump nf-azure@1.10.2 [54496ac4]
+- Bump nf-amazon@2.9.1 [fa227933]
+- Bump netty-common to version 4.1.115.Final [90623c1e]
+
 24.10.0 - 27 Oct 2024
 - Add `manifest.contributors` config option (#5322) [cf0f9690]
 - Add wave mirror and scan config [92e69776]

docs/azure.md

@@ -167,12 +167,12 @@ To specify multiple Azure machine families, use a comma separated list with glob
 process.machineType = "Standard_D*d_v5,Standard_E*d_v5"
 ```
 
-For example, the following process will create a pool of `Standard_E4d_v5` machines based when using `autoPoolMode`:
+For example, the following process will create a pool of `Standard_E8d_v5` machines based when using `autoPoolMode`:
 
 ```nextflow
 process EXAMPLE_PROCESS {
     machineType "Standard_E*d_v5"
-    cpus 16
+    cpus 8
     memory 8.GB
 
     script:

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

@@ -183,7 +183,7 @@ class SimpleFileCopyStrategy implements ScriptFileCopyStrategy {
         return """\
             IFS=\$'\\n'
             for name in \$(eval "ls -1d ${escape.join(' ')}" | sort | uniq); do
-                ${stageOutCommand('$name', targetDir, mode)} || true
+                ${stageOutCommand('$name', targetDir, mode)}
             done
             unset IFS""".stripIndent(true)
     }

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

@@ -99,7 +99,13 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    ## Capture possible errors.
+    ## Can be caused either by the task script, unstage script or after script if defined
+    local last_err=$?
+    ## capture the task error first or fallback to unstage error
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status {{exit_file}}
     set +u
     {{cleanup_cmd}}
@@ -121,13 +127,26 @@ nxf_stage() {
     {{stage_inputs}}
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
     true
-    {{unstage_controls}}
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
     {{unstage_outputs}}
 }
 
+nxf_unstage_controls() {
+    true
+    {{unstage_controls}}
+}
+
+nxf_unstage() {
+    ## Deactivate fast failure to allow uploading stdout and stderr files later
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        ## Data unstaging redirecting stdout and stderr with append mode
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a {{stdout_file}}) 3>&1 1>&2 2>&3 | tee -a {{stderr_file}})
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
+}
+
 nxf_main() {
     trap on_exit EXIT
     trap on_term TERM INT USR2

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

@@ -559,7 +559,7 @@ class BashWrapperBuilderTest extends Specification {
         binding.unstage_outputs == '''\
                 IFS=$'\\n'
                 for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
-                    nxf_fs_copy "$name" /work/dir || true
+                    nxf_fs_copy "$name" /work/dir
                 done
                 unset IFS
                 '''.stripIndent().rightTrim()
@@ -576,7 +576,7 @@ class BashWrapperBuilderTest extends Specification {
         binding.unstage_outputs == '''\
                 IFS=$'\\n'
                 for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
-                    nxf_fs_move "$name" /another/dir || true
+                    nxf_fs_move "$name" /another/dir
                 done
                 unset IFS
                 '''.stripIndent().rightTrim()

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

@@ -270,7 +270,7 @@ class SimpleFileCopyStrategyTest extends Specification {
         script == '''
                 IFS=$'\\n'
                 for name in $(eval "ls -1d simple.txt my/path/file.bam" | sort | uniq); do
-                    nxf_fs_copy "$name" /target/work\\ dir || true
+                    nxf_fs_copy "$name" /target/work\\ dir
                 done
                 unset IFS
                 '''
@@ -293,7 +293,7 @@ class SimpleFileCopyStrategyTest extends Specification {
         script == '''
                 IFS=$'\\n'
                 for name in $(eval "ls -1d simple.txt my/path/file.bam" | sort | uniq); do
-                    nxf_fs_move "$name" /target/store || true
+                    nxf_fs_move "$name" /target/store
                 done
                 unset IFS
                 '''
@@ -315,7 +315,7 @@ class SimpleFileCopyStrategyTest extends Specification {
         script == '''
                 IFS=$'\\n'
                 for name in $(eval "ls -1d simple.txt my/path/file.bam" | sort | uniq); do
-                    nxf_fs_rsync "$name" /target/work\\'s || true
+                    nxf_fs_rsync "$name" /target/work\\'s
                 done
                 unset IFS
                 '''

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

@@ -270,7 +270,10 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    local last_err=$?
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
     exit $exit_status
@@ -289,9 +292,20 @@ nxf_stage() {
     true
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
+    true
+}
+
+nxf_unstage_controls() {
     true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_unstage() {
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
 }
 
 nxf_main() {

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

@@ -81,7 +81,10 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    local last_err=$?
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
     exit $exit_status
@@ -100,9 +103,20 @@ nxf_stage() {
     true
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
+    true
+}
+
+nxf_unstage_controls() {
     true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_unstage() {
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
 }
 
 nxf_main() {

plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy

@@ -58,7 +58,7 @@ class BashWrapperBuilderWithS3Test extends Specification {
         binding.unstage_outputs == '''\
                     IFS=$'\\n'
                     for name in $(eval "ls -1d test.bam test.bai bla\\ nk.txt" | sort | uniq); do
-                        nxf_s3_upload $name s3://some/buck\\ et || true
+                        nxf_s3_upload $name s3://some/buck\\ et
                     done
                     unset IFS
                     '''.stripIndent().rightTrim()

plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy

@@ -47,7 +47,7 @@ class BashWrapperBuilderWithAzTest extends Specification {
         binding.unstage_outputs == """\
                     IFS=\$'\\n'
                     for name in \$(eval "ls -1d test.bam test.bai" | sort | uniq); do
-                        nxf_az_upload \$name '${AzHelper.toHttpUrl(target)}' || true
+                        nxf_az_upload \$name '${AzHelper.toHttpUrl(target)}'
                     done
                     unset IFS
                     """.stripIndent().rightTrim()

plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy

@@ -365,7 +365,7 @@ class GoogleLifeSciencesHelper {
         final remoteTaskDir = getRemoteTaskDir(workDir)
         def result = 'set -x; '
         result += "trap 'err=\$?; exec 1>&2; gsutil -m -q cp -R $localTaskDir/${TaskRun.CMD_LOG} ${remoteTaskDir}/${TaskRun.CMD_LOG} || true; [[ \$err -gt 0 || \$GOOGLE_LAST_EXIT_STATUS -gt 0 || \$NXF_DEBUG -gt 0 ]] && { ls -lah $localTaskDir || true; gsutil -m -q cp -R /google/ ${remoteTaskDir}; } || rm -rf $localTaskDir; exit \$err' EXIT; "
-        result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage; } >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
+        result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage;} >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
         return result
     }
 

plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy

@@ -548,7 +548,7 @@ class GoogleLifeSciencesHelperTest extends GoogleSpecification {
         def unstage = helper.getUnstagingScript(dir)
         then:
         unstage ==
-                'set -x; trap \'err=$?; exec 1>&2; gsutil -m -q cp -R /work/dir/.command.log gs://my-bucket/work/dir/.command.log || true; [[ $err -gt 0 || $GOOGLE_LAST_EXIT_STATUS -gt 0 || $NXF_DEBUG -gt 0 ]] && { ls -lah /work/dir || true; gsutil -m -q cp -R /google/ gs://my-bucket/work/dir; } || rm -rf /work/dir; exit $err\' EXIT; { cd /work/dir; bash .command.run nxf_unstage; } >> /work/dir/.command.log 2>&1'
+                'set -x; trap \'err=$?; exec 1>&2; gsutil -m -q cp -R /work/dir/.command.log gs://my-bucket/work/dir/.command.log || true; [[ $err -gt 0 || $GOOGLE_LAST_EXIT_STATUS -gt 0 || $NXF_DEBUG -gt 0 ]] && { ls -lah /work/dir || true; gsutil -m -q cp -R /google/ gs://my-bucket/work/dir; } || rm -rf /work/dir; exit $err\' EXIT; { cd /work/dir; bash .command.run nxf_unstage;} >> /work/dir/.command.log 2>&1'
     }
 
     @Unroll

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

@@ -168,7 +168,10 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    local last_err=$?
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
     exit $exit_status
@@ -192,12 +195,23 @@ nxf_stage() {
     nxf_parallel "${downloads[@]}"
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
+    true
+}
+
+nxf_unstage_controls() {
     true
     gsutil -m -q cp -R .command.out gs://bucket/work/dir/.command.out || true
     gsutil -m -q cp -R .command.err gs://bucket/work/dir/.command.err || true
     gsutil -m -q cp -R .exitcode gs://bucket/work/dir/.exitcode || true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_unstage() {
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
 }
 
 nxf_main() {

validation/awsbatch-unstage-fail.config

@@ -0,0 +1,12 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+workDir = 's3://nextflow-ci/work'
+process.executor = 'awsbatch'
+process.queue = 'nextflow-ci'
+process.container = 'quay.io/nextflow/test-aws-unstage-fail:1.0'
+aws.region = 'eu-west-1'
+aws.batch.maxTransferAttempts = 3 
+aws.batch.delayBetweenAttempts = '5 sec'

validation/awsbatch.sh

@@ -7,6 +7,13 @@ get_abs_filename() {
 
 export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 
+# Execution should fail ignoring
+$NXF_CMD run test-aws-unstage-fail.nf -c awsbatch-unstage-fail.config || true
+[[ `grep -c "Error executing process > 'test (1)'" .nextflow.log` == 1 ]] || false
+[[ `grep -c "  Essential container in task exited" .nextflow.log` == 1 ]] || false
+[[ `grep -cozP "Command exit status:\n  1" .nextflow.log` == 1 ]] || false
+[[ `grep -c "Producing a failure in aws" .nextflow.log` == 2 ]] || false
+
 $NXF_CMD run test-complexpaths.nf -c awsbatch.config
 [[ -d foo ]] || false
 [[ -e 'foo/.alpha' ]] || false
@@ -73,4 +80,4 @@ $NXF_CMD run nextflow-io/hello \
     -process.array 10 \
     -with-wave \
     -with-fusion \
-    -c awsbatch.config
+    -c awsbatch.config

validation/test-aws-unstage-fail-container/Dockerfile

@@ -0,0 +1,11 @@
+FROM ubuntu
+
+RUN apt-get update && apt-get -y install curl unzip && apt-get clean
+
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && ./aws/install && rm -rf aws*
+
+ADD fake_aws /fake_aws
+
+ENV PATH=/fake_aws/bin/:$PATH

validation/test-aws-unstage-fail-container/fake_aws/bin/aws

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+if [[ "$*" == *".command."* ]] || [[ "$*" == *".exitcode"* ]]; then
+   /usr/local/bin/aws $@
+else
+   >&2 echo "Producing a failure in aws $@"
+   exit 2
+fi
+

validation/test-aws-unstage-fail.nf

@@ -0,0 +1,16 @@
+process test {
+  input: 
+	val i
+  output: 
+        file("test${i}")
+        file("test_2_${i}")
+  script:
+  """
+  dd if=/dev/urandom of=test${i} bs=1K count=90
+  dd if=/dev/urandom of=test_2_${i} bs=1K count=90
+  """
+}
+
+workflow {
+  Channel.of(1) | test
+}