Fix chmod command to accommodate hidden files in bindir (or empty bindir) (#3247)

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

Author: abhi18av

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategy.groovy

@@ -71,7 +71,7 @@ class AwsBatchFileCopyStrategy extends SimpleFileCopyStrategy {
         // when a remote bin directory is provide managed it properly
         if( opts.remoteBinDir ) {
             result << "${opts.getAwsCli()} s3 cp --recursive --only-show-errors s3:/${opts.remoteBinDir} \$PWD/nextflow-bin\n"
-            result << "chmod +x \$PWD/nextflow-bin/*\n"
+            result << "chmod +x \$PWD/nextflow-bin/* || true\n"
             result << "export PATH=\$PWD/nextflow-bin:\$PATH\n"
         }
         // finally render the environment

plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy

@@ -326,7 +326,7 @@ class AwsBatchFileCopyStrategyTest extends Specification {
         opts.getAwsCli() >> 'aws'
         script == '''
             aws s3 cp --recursive --only-show-errors s3://foo/bar $PWD/nextflow-bin
-            chmod +x $PWD/nextflow-bin/*
+            chmod +x $PWD/nextflow-bin/* || true
             export PATH=$PWD/nextflow-bin:$PATH
             export BAR="world"
             export FOO="hola"
@@ -339,7 +339,7 @@ class AwsBatchFileCopyStrategyTest extends Specification {
         opts.getRemoteBinDir() >> '/foo/bar'
         script == '''
             /conda/bin/aws s3 cp --recursive --only-show-errors s3://foo/bar $PWD/nextflow-bin
-            chmod +x $PWD/nextflow-bin/*
+            chmod +x $PWD/nextflow-bin/* || true
             export PATH=$PWD/nextflow-bin:$PATH
             export BAR="world"
             export FOO="hola"
@@ -353,7 +353,7 @@ class AwsBatchFileCopyStrategyTest extends Specification {
         opts.getRegion() >> 'eu-west-1'
         script == '''
             /conda/bin/aws s3 cp --recursive --only-show-errors s3://foo/bar $PWD/nextflow-bin
-            chmod +x $PWD/nextflow-bin/*
+            chmod +x $PWD/nextflow-bin/* || true
             export PATH=$PWD/nextflow-bin:$PATH
             export BAR="world"
             export FOO="hola"

plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy

@@ -159,7 +159,7 @@ class AwsBatchScriptLauncherTest extends Specification {
         then:
         binding.task_env == '''\
                     aws s3 cp --recursive --only-show-errors s3://bucket/bin $PWD/nextflow-bin
-                    chmod +x $PWD/nextflow-bin/*
+                    chmod +x $PWD/nextflow-bin/* || true
                     export PATH=$PWD/nextflow-bin:$PATH
                     export FOO="xxx"
                     '''.stripIndent()

plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzFileCopyStrategy.groovy

@@ -87,7 +87,7 @@ class AzFileCopyStrategy extends SimpleFileCopyStrategy {
     String getStageInputFilesScript(Map<String, Path> inputFiles) {
         String result = ( remoteBinDir ? """\
             nxf_az_download '${AzHelper.toHttpUrl(remoteBinDir)}' \$PWD/.nextflow-bin
-            chmod +x \$PWD/.nextflow-bin/*
+            chmod +x \$PWD/.nextflow-bin/* || true
             """.stripIndent() : '' )
 
         result += 'downloads=(true)\n'

plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy

@@ -216,7 +216,7 @@ class AzFileCopyStrategyTest extends Specification {
         binding.stage_inputs == '''\
                 # stage input files
                 nxf_az_download 'http://account.blob.core.windows.net/my-data/work/remote/bin' $PWD/.nextflow-bin
-                chmod +x $PWD/.nextflow-bin/*
+                chmod +x $PWD/.nextflow-bin/* || true
                 downloads=(true)
                 
                 nxf_parallel "${downloads[@]}"

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

@@ -155,7 +155,7 @@ class GoogleLifeSciencesFileCopyStrategy extends SimpleFileCopyStrategy {
             copy.remove('PATH')
         // when a remote bin directory is provide managed it properly
         if( config.remoteBinDir ) {
-            result << "chmod +x $localTaskDir/nextflow-bin/*\n"
+            result << "chmod +x $localTaskDir/nextflow-bin/* || true\n"
             result << "export PATH=$localTaskDir/nextflow-bin:\$PATH\n"
         }
         // finally render the environment

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

@@ -219,7 +219,7 @@ class GoogleLifeSciencesFileCopyStrategyTest extends GoogleSpecification {
         def envScript = strategy.getEnvScript([FOO:1, BAR: 2, PATH: 3], false)
         then:
         envScript == '''\
-                chmod +x /work/xx/yy/nextflow-bin/*
+                chmod +x /work/xx/yy/nextflow-bin/* || true
                 export PATH=/work/xx/yy/nextflow-bin:$PATH
                 export BAR="2"
                 export FOO="1"

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

@@ -56,7 +56,7 @@ class GoogleLifeSciencesScriptLauncherTest extends GoogleSpecification {
         binding.stage_cmd == null
         binding.unstage_cmd == null
         binding.task_env == '''\
-                chmod +x /work/xx/yy/nextflow-bin/*
+                chmod +x /work/xx/yy/nextflow-bin/* || true
                 export PATH=/work/xx/yy/nextflow-bin:$PATH
                 export FOO="xxx"
                 '''.stripIndent()