From 71932f9d118a8c87634e4889cb99be5737ea2d37 Mon Sep 17 00:00:00 2001
From: Jorge Aguilera <jorge.aguilera@seqera.io>
Date: Wed, 16 Nov 2022 13:24:45 +0100
Subject: [PATCH 01/13] remove capsule and create a single jar

Signed-off-by: Jorge Aguilera <jorge.aguilera@seqera.io>
---
 modules/nextflow/build.gradle |  17 +++++
 nextflow                      |  32 +++------
 packing.gradle                | 119 +---------------------------------
 3 files changed, 28 insertions(+), 140 deletions(-)

diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index 3e3f156a7d..898a17080c 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -1,3 +1,6 @@
+plugins {
+    id "com.github.johnrengelman.shadow" version "7.1.2"
+}
 apply plugin: 'groovy'
 apply plugin: 'application'
 
@@ -70,3 +73,17 @@ application {
 run{
     args( (project.hasProperty("runCmd") ? project.findProperty("runCmd") : "set a cmd to run").split(' ') )
 }
+
+shadowJar {
+    archiveClassifier='one'
+    manifest {
+        attributes 'Main-Class': "$mainClassName"
+    }
+    mergeServiceFiles()
+    mergeGroovyExtensionModules()
+    doLast {
+        ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: releaseDir, overwrite: true)
+        ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: nextflowDir, overwrite: true)
+        println "\n+ Nextflow package copied to: $releaseDir"
+    }
+}
\ No newline at end of file
diff --git a/nextflow b/nextflow
index 0b9752caa0..e77dc5bbac 100755
--- a/nextflow
+++ b/nextflow
@@ -135,12 +135,12 @@ function install() {
 function launch_nextflow() {
     # the launch command line
     local cmdline=()
-    # remove leading and trailing double-quotes 
+    # remove leading and trailing double-quotes
     for x in "${launcher[@]}"; do
         x="${x%\"}"
         x="${x#\"}"
-        cmdline+=("$x") 
-    done 
+        cmdline+=("$x")
+    done
 
     if [[ "$bg" ]]; then
       local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
@@ -237,9 +237,6 @@ if [[ "$dockerize" ]]; then
   exit 1
 fi
 
-CAPSULE_LOG=${CAPSULE_LOG:=''}
-CAPSULE_RESET=${CAPSULE_RESET:=''}
-CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}
 
 NXF_PACK=one
 NXF_MODE=${NXF_MODE:-''}
@@ -254,11 +251,11 @@ NXF_HOST=${HOSTNAME:-localhost}
 
 # Determine the path to this file
 if [[ $NXF_PACK = all ]]; then
-    NXF_BIN=$(which "$0" 2>/dev/null)
-    [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
+    echo "NXF_PACK=all is deprecated"
+    exit 1
 fi
 
-# use nextflow custom java home path 
+# use nextflow custom java home path
 if [[ "$NXF_JAVA_HOME" ]]; then
   JAVA_HOME="$NXF_JAVA_HOME"
   unset JAVA_CMD
@@ -333,14 +330,11 @@ fi
 
 COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
 declare -a JAVA_OPTS=()
-JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD" -Dcom.sun.security.enableAIAcaIssuers=true)
+JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcom.sun.security.enableAIAcaIssuers=true)
 if [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=(-Djava.awt.headless=true)
 fi
 
-[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
-[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
-[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
 [[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
 [[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
 [[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
@@ -349,7 +343,6 @@ fi
 [[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP")
 [[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}")
 export JAVA_CMD
-export CAPSULE_CACHE_DIR
 export NXF_PLUGINS_DIR
 export NXF_PLUGINS_MODE
 export NXF_PLUGINS_DEFAULT
@@ -363,7 +356,7 @@ else MD5=''
 fi
 
 # when no md5 command is available fallback on default execution
-if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
+if [ ! "$MD5" ]; then
     launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
     launch_nextflow
     exit 1
@@ -393,13 +386,8 @@ fi
 if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
     declare -a launcher="($(cat "$LAUNCH_FILE"))"
 else
-    # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
-    cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
-    [[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
-
-    # first string between double quotes is the full path to java, also blank spaces are included
-    # remainder string are arguments
-    # we extract first part into `cmd_base`` and remainder into `cmd_tail`` and convert them to array as previous version
+    # otherwise parse the command and get the result classpath in the 'launcher' and save it to a file
+    cli=("\"$JAVA_CMD\"" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")
     cmd_pattern='"([^"]*)"(.*)'
     [[ "${cli[@]}" =~ $cmd_pattern ]]
     cmd_base=(${BASH_REMATCH[1]})
diff --git a/packing.gradle b/packing.gradle
index a9b142f870..75e2f68784 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -1,5 +1,4 @@
 configurations {
-    capsule
     defaultCfg.extendsFrom api 
     //provided
     console.extendsFrom defaultCfg
@@ -17,9 +16,6 @@ dependencies {
     defaultCfg "org.apache.ivy:ivy:2.3.0"
     // default cfg = runtime + httpfs + amazon + tower client
     defaultCfg project(':nf-httpfs')
-    // Capsule manages the fat jar building process
-    capsule 'io.nextflow:capsule:1.1.1'
-    capsule 'io.nextflow:capsule-maven:1.0.3.2'
     console project(':plugins:nf-console')
     ga4gh   project(':plugins:nf-ga4gh')
     google  project(':plugins:nf-google')
@@ -91,124 +87,11 @@ protected coordinates( it ) {
     throw new IllegalArgumentException("Not a valid dependency object [${it?.class?.name}]: $it")
 }
 
-/*
- * Default nextflow package. It contains the capsule loader
- */
-task packOne(type: Jar) {
-    dependsOn configurations.capsule, configurations.defaultCfg
-    archiveName = "nextflow-${version}-one.jar"
-
-    from (configurations.capsule.collect { zipTree(it) })
-
-    // main manifest attributes
-    def deps = resolveDeps('defaultCfg')
-
-    manifest.attributes(
-                'Main-Class'        : 'NextflowLoader',
-                'Application-Name'  : 'nextflow',
-                'Application-Class' : mainClassName,
-                'Application-Version': version,
-                'Min-Java-Version'  : '1.8.0',
-                'Caplets'           : 'MavenCapsule',
-                'Dependencies'      : deps
-    )
-
-    // enable snapshot dependencies lookup
-    if( version.endsWith('-SNAPSHOT') ) {
-        manifest.attributes 'Allow-Snapshots': true
-        manifest.attributes 'Repositories': 'local https://oss.sonatype.org/content/repositories/snapshots central seqera'
-    }
-    else {
-        manifest.attributes 'Repositories': 'central seqera'
-    }
-
-    doLast {
-        ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: releaseDir, overwrite: true)
-        ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: nextflowDir, overwrite: true)
-        println "\n+ Nextflow package `ONE` copied to: $releaseDir"
-    }
-}
-
-task packAll(type: Jar) {
-    dependsOn configurations.capsule, configurations.defaultCfg
-    archiveName = "nextflow-${version}-all.jar"
-
-    from jar // embed our application jar
-    from (configurations.amazon + configurations.google + configurations.tower)
-    from (configurations.capsule.collect { zipTree(it) })
-    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-    
-    manifest.attributes( 'Main-Class'        : 'NextflowLoader',
-                          'Application-Name'  : 'nextflow-all',
-                          'Application-Class' : mainClassName,
-                          'Application-Version': version,
-                          'Min-Java-Version'  : '1.8.0'
-                          )
-
-    manifest.attributes('Main-Class': 'NextflowLoader', 'amazon')
-    manifest.attributes('Main-Class': 'NextflowLoader', 'google')
-
-    if( project.hasProperty('GA4GH') ) {
-        println "The build will include GA4GH dependencies."
-        from(configurations.ga4gh)
-        manifest.attributes('Main-Class': 'CapsuleLoader', 'ga4gh')
-    }
-
-    doLast {
-        file(releaseDir).mkdir()
-        // cleanup
-        def source = file("$buildDir/libs/nextflow-${version}-all.jar")
-        def target = file("$releaseDir/nextflow-${version}-all"); target.delete()
-        // append the big jar
-        target.withOutputStream {
-            it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=all')
-            it << new FileInputStream(source)
-        }
-        // execute permission
-        "chmod +x $target".execute()
-        // done
-        println "+ Nextflow package `ALL` copied to: $releaseDir\n"
-    }
-}
-
-task packCore(type: Jar) {
-    dependsOn configurations.capsule, configurations.defaultCfg
-    archiveName = "nextflow-${version}-core.jar"
-
-    from jar // embed our application jar
-    from (configurations.defaultCfg)
-    from (configurations.capsule.collect { zipTree(it) })
-    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-
-    manifest.attributes( 'Main-Class'        : 'NextflowLoader',
-            'Application-Name'  : 'nextflow-core',
-            'Application-Class' : mainClassName,
-            'Application-Version': version,
-            'Min-Java-Version'  : '1.8.0'
-    )
-
-    doLast {
-        file(releaseDir).mkdir()
-        // cleanup
-        def source = file("$buildDir/libs/nextflow-${version}-core.jar")
-        def target = file("$releaseDir/nextflow-${version}-core"); target.delete()
-        // append the big jar
-        target.withOutputStream {
-            it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=all')
-            it << new FileInputStream(source)
-        }
-        // execute permission
-        "chmod +x $target".execute()
-        // done
-        println "+ Nextflow package `CORE` copied to: $releaseDir\n"
-    }
-}
-
 
 /*
  * Compile and pack all packages
  */
-task pack( dependsOn: [packOne, packAll]) {
+task pack( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
 
 }
 

From fc02a6e41d3800283033efa61962964fc9968567 Mon Sep 17 00:00:00 2001
From: Jorge Aguilera <jorge.aguilera@seqera.io>
Date: Wed, 16 Nov 2022 14:44:25 +0100
Subject: [PATCH 02/13] remove capsule and create a single jar

Signed-off-by: Jorge Aguilera <jorge.aguilera@seqera.io>
---
 Makefile                      | 6 +++---
 modules/nextflow/build.gradle | 5 -----
 packing.gradle                | 6 +++++-
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index e0d25170a0..3ef2ca89c6 100644
--- a/Makefile
+++ b/Makefile
@@ -95,16 +95,16 @@ upload:
 # Create self-contained distribution package
 #
 pack:
-	BUILD_PACK=1 ./gradlew packAll
+	BUILD_PACK=1 ./gradlew pack
 
 packCore:
-	BUILD_PACK=1 ./gradlew packCore
+	BUILD_PACK=1 ./gradlew pack
 
 #
 # Create self-contained distribution package, including GA4GH support and associated dependencies
 #
 packGA4GH:
-	BUILD_PACK=1 ./gradlew -PGA4GH packAll
+	BUILD_PACK=1 ./gradlew -PGA4GH pack
 
 #
 # Upload NF launcher to nextflow.io web site
diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index 40dba1abb6..677e20e9cb 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -81,9 +81,4 @@ shadowJar {
     }
     mergeServiceFiles()
     mergeGroovyExtensionModules()
-    doLast {
-        ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: releaseDir, overwrite: true)
-        ant.copy(file: "$buildDir/libs/nextflow-${version}-one.jar", todir: nextflowDir, overwrite: true)
-        println "\n+ Nextflow package copied to: $releaseDir"
-    }
 }
\ No newline at end of file
diff --git a/packing.gradle b/packing.gradle
index 75e2f68784..4b7872110f 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -92,7 +92,11 @@ protected coordinates( it ) {
  * Compile and pack all packages
  */
 task pack( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
-
+    doLast {
+        ant.copy(file: "modules/nextflow/build/libs/nextflow-${version}-one.jar", todir: releaseDir, overwrite: true)
+        ant.copy(file: "modules/nextflow/build/libs/nextflow-${version}-one.jar", todir: nextflowDir, overwrite: true)
+        println "\n+ Nextflow package `ONE` copied to: $releaseDir"
+    }
 }
 
 

From 4b1f00ad8b9c9af180451266183af055324b221e Mon Sep 17 00:00:00 2001
From: Jorge Aguilera <jorge.aguilera@seqera.io>
Date: Wed, 16 Nov 2022 16:48:15 +0100
Subject: [PATCH 03/13] make launcher compatible with previous and new versions

Signed-off-by: Jorge Aguilera <jorge.aguilera@seqera.io>
---
 nextflow | 42 +++++++++++++++++++++++++++++++++++++-----
 1 file changed, 37 insertions(+), 5 deletions(-)

diff --git a/nextflow b/nextflow
index e77dc5bbac..035c7cc7e7 100755
--- a/nextflow
+++ b/nextflow
@@ -26,6 +26,14 @@ NXF_DIST=${NXF_DIST:-$NXF_HOME/framework}
 NXF_CLI="$0 $@"
 NXF_CLI_OPTS=${NXF_CLI_OPTS:-}
 
+NXF_CAPSULE_LAUNCHER=1
+NXF_V=$(echo $NXF_VER| cut -d'.' -f1)
+NXF_R=$(echo $NXF_VER| cut -d'.' -f2)
+if [[ NXF_V -ge 22 ]] && [[ NXF_R -ge 11 ]]; then
+  # from version 22.11.X we will use a fat jar and remove capsule dependency
+  unset NXF_CAPSULE_LAUNCHER
+fi
+
 export NXF_CLI
 export NXF_ORG
 export NXF_HOME
@@ -70,7 +78,7 @@ function get() {
         exit 1
     fi
 
-    printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. "
+    printf "Downloading nextflow dependencies using $GET. It may require a few seconds, please wait .. "
     eval $GET; status=$?
     printf "\r\033[K"
     if [ $status -ne 0 ]; then
@@ -237,6 +245,9 @@ if [[ "$dockerize" ]]; then
   exit 1
 fi
 
+CAPSULE_LOG=${CAPSULE_LOG:=''}
+CAPSULE_RESET=${CAPSULE_RESET:=''}
+CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}
 
 NXF_PACK=one
 NXF_MODE=${NXF_MODE:-''}
@@ -251,8 +262,13 @@ NXF_HOST=${HOSTNAME:-localhost}
 
 # Determine the path to this file
 if [[ $NXF_PACK = all ]]; then
+  if [[ $NXF_CAPSULE_LAUNCHER ]]; then
+    NXF_BIN=$(which "$0" 2>/dev/null)
+    [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
+  else
     echo "NXF_PACK=all is deprecated"
     exit 1
+  fi
 fi
 
 # use nextflow custom java home path
@@ -330,11 +346,16 @@ fi
 
 COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
 declare -a JAVA_OPTS=()
-JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcom.sun.security.enableAIAcaIssuers=true)
+JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD" -Dcom.sun.security.enableAIAcaIssuers=true)
 if [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=(-Djava.awt.headless=true)
 fi
 
+if [[ $NXF_CAPSULE_LAUNCHER ]]; then
+  [[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
+  [[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
+  [[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
+fi
 [[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
 [[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
 [[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
@@ -343,6 +364,7 @@ fi
 [[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP")
 [[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}")
 export JAVA_CMD
+export CAPSULE_CACHE_DIR
 export NXF_PLUGINS_DIR
 export NXF_PLUGINS_MODE
 export NXF_PLUGINS_DEFAULT
@@ -356,7 +378,7 @@ else MD5=''
 fi
 
 # when no md5 command is available fallback on default execution
-if [ ! "$MD5" ]; then
+if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
     launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
     launch_nextflow
     exit 1
@@ -386,8 +408,18 @@ fi
 if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
     declare -a launcher="($(cat "$LAUNCH_FILE"))"
 else
-    # otherwise parse the command and get the result classpath in the 'launcher' and save it to a file
-    cli=("\"$JAVA_CMD\"" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")
+    if [[ $NXF_CAPSULE_LAUNCHER ]]; then
+      # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
+      cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
+    [[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
+    else
+      # otherwise parse the command and get the result classpath in the 'launcher' and save it to a file
+      cli=("\"$JAVA_CMD\"" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")
+    fi
+
+    # first string between double quotes is the full path to java, also blank spaces are included
+    # remainder string are arguments
+    # we extract first part into `cmd_base`` and remainder into `cmd_tail`` and convert them to array as previous version
     cmd_pattern='"([^"]*)"(.*)'
     [[ "${cli[@]}" =~ $cmd_pattern ]]
     cmd_base=(${BASH_REMATCH[1]})

From 031a6194b360848969fda55408426f759fdbdddd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 8 Jun 2024 17:13:35 +0200
Subject: [PATCH 04/13] Bump version

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION  | 2 +-
 nextflow | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/VERSION b/VERSION
index 11300bc91f..4369e7eda7 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-24.04.2
+24.05.0-edge
diff --git a/nextflow b/nextflow
index 7b5ff0ac84..8ddb456368 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'24.04.2'}
+NXF_VER=${NXF_VER:-'24.05.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
@@ -29,8 +29,7 @@ NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
 NXF_CAPSULE_LAUNCHER=1
 NXF_V=$(echo $NXF_VER| cut -d'.' -f1)
 NXF_R=$(echo $NXF_VER| cut -d'.' -f2)
-if [[ NXF_V -ge 22 ]] && [[ NXF_R -ge 11 ]]; then
-  # from version 22.11.X we will use a fat jar and remove capsule dependency
+if [[ NXF_V -ge 24 ]] && [[ NXF_R -ge 5 ]]; then
   unset NXF_CAPSULE_LAUNCHER
 fi
 

From ba16f24dc2640b5f3b632619ee69f84d1f7f90d4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 27 Jul 2024 17:10:32 +0200
Subject: [PATCH 05/13] Bump shadowJar 8.1.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/build.gradle | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index 672840cc7d..ff7f48dc83 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -1,5 +1,5 @@
 plugins {
-    id "com.github.johnrengelman.shadow" version "7.1.2"
+    id "com.github.johnrengelman.shadow" version "8.1.1"
 }
 apply plugin: 'groovy'
 apply plugin: 'application'
@@ -83,4 +83,4 @@ shadowJar {
     }
     mergeServiceFiles()
     mergeGroovyExtensionModules()
-}
\ No newline at end of file
+}

From b518fae3c3927b8b0e143b979f7d49cb42b35f77 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 27 Jul 2024 20:18:11 +0200
Subject: [PATCH 06/13] wip

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 Makefile                    |  4 +--
 VERSION                     |  2 +-
 modules/nf-all/build.gradle | 53 +++++++++++++++++++++++++++++++++++++
 nextflow                    |  7 +----
 packing.gradle              | 19 +++++++++++++
 settings.gradle             |  1 +
 6 files changed, 77 insertions(+), 9 deletions(-)
 create mode 100644 modules/nf-all/build.gradle

diff --git a/Makefile b/Makefile
index f07921c1e1..7e5f088f94 100644
--- a/Makefile
+++ b/Makefile
@@ -97,8 +97,8 @@ upload:
 pack:
 	BUILD_PACK=1 ./gradlew pack
 
-packCore:
-	BUILD_PACK=1 ./gradlew pack
+packAll:
+	BUILD_PACK=1 ./gradlew packAll
 
 #
 # Upload NF launcher to nextflow.io web site
diff --git a/VERSION b/VERSION
index 4e8327ae10..d4c0237907 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-24.06.0-edge
+24.07.0-edge
diff --git a/modules/nf-all/build.gradle b/modules/nf-all/build.gradle
new file mode 100644
index 0000000000..e153797d86
--- /dev/null
+++ b/modules/nf-all/build.gradle
@@ -0,0 +1,53 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+plugins {
+    id "com.github.johnrengelman.shadow" version "8.1.1"
+}
+apply plugin: 'groovy'
+apply plugin: 'application'
+
+group = 'io.nextflow'
+version = rootProject.file('VERSION').text.trim()
+
+dependencies {
+    implementation project(':nextflow')
+    implementation project(':plugins:nf-amazon')
+    implementation project(':plugins:nf-azure')
+    implementation project(':plugins:nf-cloudcache')
+    implementation project(':plugins:nf-codecommit')
+    implementation project(':plugins:nf-console')
+    implementation project(':plugins:nf-google')
+    implementation project(':plugins:nf-tower')
+    implementation project(':plugins:nf-wave')
+}
+
+application {
+    mainClass = 'nextflow.cli.Launcher'
+}
+
+shadowJar {
+    zip64 = true
+    archiveBaseName.set('nextflow')
+    archiveVersion.set(version as String)
+    archiveClassifier.set('all')
+    manifest {
+        attributes 'Main-Class': "$mainClassName"
+    }
+    mergeServiceFiles()
+    mergeGroovyExtensionModules()
+}
diff --git a/nextflow b/nextflow
index 8af75f036a..449debafdc 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'24.06.0-edge'}
+NXF_VER=${NXF_VER:-'24.07.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
@@ -263,13 +263,8 @@ NXF_HOST=${HOSTNAME:-localhost}
 
 # Determine the path to this file
 if [[ $NXF_PACK = all ]]; then
-  if [[ $NXF_CAPSULE_LAUNCHER ]]; then
     NXF_BIN=$(which "$0" 2>/dev/null)
     [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
-  else
-    echo "NXF_PACK=all is deprecated"
-    exit 1
-  fi
 fi
 
 # use nextflow custom java home path
diff --git a/packing.gradle b/packing.gradle
index c41664738d..041b294d54 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -98,6 +98,25 @@ task pack( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
     }
 }
 
+task packAll( dependsOn: [clean, compile, ":nf-all:shadowJar"]) {
+
+    doLast {
+        file(releaseDir).mkdirs()
+        // cleanup
+        def source = file("modules/nf-all/build/libs/nextflow-${version}-all.jar")
+        def target = file("$releaseDir/nextflow-${version}-all"); target.delete()
+        // append the big jar
+        target.withOutputStream {
+            it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=all')
+            it << new FileInputStream(source)
+        }
+        // execute permission
+        "chmod +x $target".execute()
+        // done
+        println "+ Nextflow package `ALL` copied to: $releaseDir\n"
+    }
+}
+
 
 task deploy( type: Exec, dependsOn: [clean, compile, pack]) {
 
diff --git a/settings.gradle b/settings.gradle
index c9900fd00f..300028d13e 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -26,6 +26,7 @@ rootProject.name = 'nextflow-prj'
 include 'nextflow'
 include 'nf-commons'
 include 'nf-httpfs'
+include 'nf-all'
 
 rootProject.children.each { prj ->
     prj.projectDir = new File("$rootDir/modules/$prj.name")

From 3cae56995aa824a984b57aa185343915892b07bd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 29 Jul 2024 12:25:26 +0200
Subject: [PATCH 07/13] wip

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md              |  3 ---
 modules/nf-all/build.gradle | 53 -------------------------------------
 nextflow                    |  5 ++--
 settings.gradle             |  1 -
 4 files changed, 3 insertions(+), 59 deletions(-)
 delete mode 100644 modules/nf-all/build.gradle

diff --git a/docs/config.md b/docs/config.md
index ba97797cdb..e63aedd1dd 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1894,9 +1894,6 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_CHARLIECLOUD_CACHEDIR`
 : Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
 
-`NXF_CLASSPATH`
-: Allows the extension of the Java runtime classpath with extra JAR files or class folders.
-
 `NXF_CLOUDCACHE_PATH`
 : :::{versionadded} 23.07.0-edge
   :::
diff --git a/modules/nf-all/build.gradle b/modules/nf-all/build.gradle
deleted file mode 100644
index e153797d86..0000000000
--- a/modules/nf-all/build.gradle
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright 2013-2024, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-plugins {
-    id "com.github.johnrengelman.shadow" version "8.1.1"
-}
-apply plugin: 'groovy'
-apply plugin: 'application'
-
-group = 'io.nextflow'
-version = rootProject.file('VERSION').text.trim()
-
-dependencies {
-    implementation project(':nextflow')
-    implementation project(':plugins:nf-amazon')
-    implementation project(':plugins:nf-azure')
-    implementation project(':plugins:nf-cloudcache')
-    implementation project(':plugins:nf-codecommit')
-    implementation project(':plugins:nf-console')
-    implementation project(':plugins:nf-google')
-    implementation project(':plugins:nf-tower')
-    implementation project(':plugins:nf-wave')
-}
-
-application {
-    mainClass = 'nextflow.cli.Launcher'
-}
-
-shadowJar {
-    zip64 = true
-    archiveBaseName.set('nextflow')
-    archiveVersion.set(version as String)
-    archiveClassifier.set('all')
-    manifest {
-        attributes 'Main-Class': "$mainClassName"
-    }
-    mergeServiceFiles()
-    mergeGroovyExtensionModules()
-}
diff --git a/nextflow b/nextflow
index 449debafdc..661df08986 100755
--- a/nextflow
+++ b/nextflow
@@ -256,10 +256,11 @@ NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar}
 NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR}
 NXF_PATH=$(dirname "$NXF_BIN")
 NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR}
-NXF_GRAB=${NXF_GRAB:-''}
-NXF_CLASSPATH=${NXF_CLASSPATH:-''}
 NXF_HOST=${HOSTNAME:-localhost}
 [[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST}
+# both NXF_GRAB and NXF_CLASSPATH are not supported any more as of version 24.04.7-edge
+NXF_GRAB=${NXF_GRAB:-''}
+NXF_CLASSPATH=${NXF_CLASSPATH:-''}
 
 # Determine the path to this file
 if [[ $NXF_PACK = all ]]; then
diff --git a/settings.gradle b/settings.gradle
index 300028d13e..c9900fd00f 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -26,7 +26,6 @@ rootProject.name = 'nextflow-prj'
 include 'nextflow'
 include 'nf-commons'
 include 'nf-httpfs'
-include 'nf-all'
 
 rootProject.children.each { prj ->
     prj.projectDir = new File("$rootDir/modules/$prj.name")

From 68895a39cf6acfc36770bd383690bb2f76e13dec Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 29 Jul 2024 12:48:04 +0200
Subject: [PATCH 08/13] Allow plugins in self-contained mode

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/nextflow/plugin/PluginsFacade.groovy | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index 01df157273..4bf9640577 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -318,8 +318,8 @@ class PluginsFacade implements PluginStateListener {
     }
 
     void start( String pluginId ) {
-        if( isSelfContained() && defaultPlugins.hasPlugin(pluginId) ) {
-            log.debug "Plugin 'start' is not required in self-contained mode -- ignoring for plugin: $pluginId"
+        if( isEmbedded() && defaultPlugins.hasPlugin(pluginId) ) {
+            log.debug "Plugin 'start' is not required in embedded mode -- ignoring for plugin: $pluginId"
             return
         }
 
@@ -327,8 +327,8 @@ class PluginsFacade implements PluginStateListener {
     }
 
     void start(PluginSpec plugin) {
-        if( isSelfContained() && defaultPlugins.hasPlugin(plugin.id) ) {
-            log.debug "Plugin 'start' is not required in self-contained mode -- ignoring for plugin: $plugin.id"
+        if( isEmbedded() && defaultPlugins.hasPlugin(plugin.id) ) {
+            log.debug "Plugin 'start' is not required in embedded mode -- ignoring for plugin: $plugin.id"
             return
         }
 
@@ -346,19 +346,19 @@ class PluginsFacade implements PluginStateListener {
     }
 
     /**
-     * @return {@code true} when running in self-contained mode ie. the nextflow distribution
+     * @return {@code true} when running in embedded mode ie. the nextflow distribution
      * include also plugin libraries. When running is this mode, plugins should not be started
      * and cannot be updated. 
      */
-    protected boolean isSelfContained() {
-        return env.get('NXF_PACK')=='all' || embedded
+    protected boolean isEmbedded() {
+        return embedded
     }
 
     protected List<PluginSpec> pluginsRequirement(Map config) {
         def specs = parseConf(config)
-        if( isSelfContained() && specs ) {
+        if( isEmbedded() && specs ) {
             // custom plugins are not allowed for nextflow self-contained package
-            log.warn "Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: ${specs.join(',')}"
+            log.warn "Nextflow embedded mode only core plugins -- User config plugins will be ignored: ${specs.join(',')}"
             return Collections.emptyList()
         }
         if( specs ) {
@@ -441,7 +441,7 @@ class PluginsFacade implements PluginStateListener {
     boolean startIfMissing(String pluginId) {
         if( env.NXF_PLUGINS_DEFAULT == 'false' )
             return false
-        if( isSelfContained() && defaultPlugins.hasPlugin(pluginId) )
+        if( isEmbedded() && defaultPlugins.hasPlugin(pluginId) )
             return false
 
         if( isStarted(pluginId) )

From d5d70d95cc7b661f53f50a9e71881a262298e11c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 29 Jul 2024 13:12:20 +0200
Subject: [PATCH 09/13] Rename NXF_CAPSULE_LAUNCHER to NXF_LEGACY_LAUNCHER

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 nextflow | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/nextflow b/nextflow
index 661df08986..36ff944087 100755
--- a/nextflow
+++ b/nextflow
@@ -26,11 +26,11 @@ NXF_CLI="$0 $@"
 NXF_CLI_OPTS=${NXF_CLI_OPTS:-}
 NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
 
-NXF_CAPSULE_LAUNCHER=1
-NXF_V=$(echo $NXF_VER| cut -d'.' -f1)
-NXF_R=$(echo $NXF_VER| cut -d'.' -f2)
-if [[ NXF_V -ge 24 ]] && [[ NXF_R -ge 5 ]]; then
-  unset NXF_CAPSULE_LAUNCHER
+NXF_LEGACY_LAUNCHER=1
+NXF_V1=$(echo $NXF_VER| cut -d'.' -f1)
+NXF_V2=$(echo $NXF_VER| cut -d'.' -f2)
+if [[ NXF_V1 -ge 24 ]] && [[ NXF_V2 -ge 7 ]]; then
+  unset NXF_LEGACY_LAUNCHER
 fi
 
 export NXF_CLI
@@ -354,7 +354,7 @@ if [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=(-Djava.awt.headless=true)
 fi
 
-if [[ $NXF_CAPSULE_LAUNCHER ]]; then
+if [[ $NXF_LEGACY_LAUNCHER ]]; then
   [[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
   [[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
   [[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
@@ -411,10 +411,10 @@ LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
 if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ] && [[ "$remote_debug" -ne 1 ]]; then
     declare -a launcher="($(cat "$LAUNCH_FILE"))"
 else
-    if [[ $NXF_CAPSULE_LAUNCHER ]]; then
+    if [[ $NXF_LEGACY_LAUNCHER ]]; then
       # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
       cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
-    [[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
+      [[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
     else
       # otherwise parse the command and get the result classpath in the 'launcher' and save it to a file
       cli=("\"$JAVA_CMD\"" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")
@@ -460,6 +460,7 @@ else
       launcher+=("${cmd_tail[@]}")
     fi
 
+    if [[ $NXF_LEGACY_LAUNCHER ]]; then
     # Don't show errors if the LAUNCH_FILE can't be created
     if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
         STR=''
@@ -470,6 +471,7 @@ else
     else
         echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?"
     fi
+    fi
 
 fi
 

From 3aec12f4a806e42be55dd288719d244a87d063e7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 29 Jul 2024 13:12:50 +0200
Subject: [PATCH 10/13] Rename pack "all" to "dist"

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 Makefile       |  3 ---
 nextflow       |  2 +-
 packing.gradle | 25 ++++++++++++++++---------
 3 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/Makefile b/Makefile
index 7e5f088f94..4a12211e00 100644
--- a/Makefile
+++ b/Makefile
@@ -97,9 +97,6 @@ upload:
 pack:
 	BUILD_PACK=1 ./gradlew pack
 
-packAll:
-	BUILD_PACK=1 ./gradlew packAll
-
 #
 # Upload NF launcher to nextflow.io web site
 #
diff --git a/nextflow b/nextflow
index 36ff944087..d0c8c2d78d 100755
--- a/nextflow
+++ b/nextflow
@@ -263,7 +263,7 @@ NXF_GRAB=${NXF_GRAB:-''}
 NXF_CLASSPATH=${NXF_CLASSPATH:-''}
 
 # Determine the path to this file
-if [[ $NXF_PACK = all ]]; then
+if [[ $NXF_PACK = dist ]]; then
     NXF_BIN=$(which "$0" 2>/dev/null)
     [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
 fi
diff --git a/packing.gradle b/packing.gradle
index 041b294d54..ccbfdaf40e 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -90,33 +90,40 @@ protected coordinates( it ) {
 /*
  * Compile and pack all packages
  */
-task pack( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
+task packOne( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
     doLast {
-        ant.copy(file: "modules/nextflow/build/libs/nextflow-${version}-one.jar", todir: releaseDir, overwrite: true)
-        ant.copy(file: "modules/nextflow/build/libs/nextflow-${version}-one.jar", todir: nextflowDir, overwrite: true)
-        println "\n+ Nextflow package `ONE` copied to: $releaseDir"
+        def source = "modules/nextflow/build/libs/nextflow-${version}-one.jar"
+        ant.copy(file: source, todir: releaseDir, overwrite: true)
+        ant.copy(file: source, todir: nextflowDir, overwrite: true)
+        println "\n+ Nextflow package `ONE` copied to: $releaseDir/nextflow-${version}-one.jar"
     }
 }
 
-task packAll( dependsOn: [clean, compile, ":nf-all:shadowJar"]) {
+task packDist( dependsOn: [clean, compile, ":nextflow:shadowJar"]) {
 
     doLast {
         file(releaseDir).mkdirs()
         // cleanup
-        def source = file("modules/nf-all/build/libs/nextflow-${version}-all.jar")
-        def target = file("$releaseDir/nextflow-${version}-all"); target.delete()
+        def source = file("modules/nextflow/build/libs/nextflow-${version}-one.jar")
+        def target = file("$releaseDir/nextflow-${version}-dist"); target.delete()
         // append the big jar
         target.withOutputStream {
-            it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=all')
+            it << file('nextflow').text.replaceAll(/NXF_PACK\=.*/, 'NXF_PACK=dist')
             it << new FileInputStream(source)
         }
         // execute permission
         "chmod +x $target".execute()
         // done
-        println "+ Nextflow package `ALL` copied to: $releaseDir\n"
+        println "+ Nextflow package `ALL` copied to: $target\n"
     }
 }
 
+/*
+ * Compile and pack all packages
+ */
+task pack( dependsOn: [packOne, packDist]) {
+
+}
 
 task deploy( type: Exec, dependsOn: [clean, compile, pack]) {
 

From 6784c7026adf8f4008cb9d77586726f09990be03 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 29 Jul 2024 15:57:29 +0200
Subject: [PATCH 11/13] Update nextflow [ci skip]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 nextflow | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow b/nextflow
index d0c8c2d78d..d3c74d5a6d 100755
--- a/nextflow
+++ b/nextflow
@@ -77,7 +77,7 @@ function get() {
         exit 1
     fi
 
-    printf "Downloading nextflow dependencies using $GET. It may require a few seconds, please wait .. "
+    printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. "
     eval $GET; status=$?
     printf "\r\033[K"
     if [ $status -ne 0 ]; then

From bb4d02636f067c1d7d49dedb95b48f2d87284613 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 29 Jul 2024 16:12:26 +0200
Subject: [PATCH 12/13] Update nextflow [ci skip]

Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 nextflow | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nextflow b/nextflow
index d3c74d5a6d..86214ec377 100755
--- a/nextflow
+++ b/nextflow
@@ -27,9 +27,9 @@ NXF_CLI_OPTS=${NXF_CLI_OPTS:-}
 NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
 
 NXF_LEGACY_LAUNCHER=1
-NXF_V1=$(echo $NXF_VER| cut -d'.' -f1)
-NXF_V2=$(echo $NXF_VER| cut -d'.' -f2)
-if [[ NXF_V1 -ge 24 ]] && [[ NXF_V2 -ge 7 ]]; then
+NXF_VER_MAJOR=$(echo $NXF_VER| cut -d'.' -f1)
+NXF_VER_MINOR=$(echo $NXF_VER| cut -d'.' -f2)
+if [[ NXF_VER_MAJOR -ge 24 ]] && [[ NXF_VER_MINOR -ge 7 ]]; then
   unset NXF_LEGACY_LAUNCHER
 fi
 

From 909a9f3e5adb01e6bc7af7adbb77c71a4f255a89 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 30 Jul 2024 13:10:08 +0200
Subject: [PATCH 13/13] Minor change [ci skip]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 nextflow | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nextflow b/nextflow
index 86214ec377..9b7395b7a9 100755
--- a/nextflow
+++ b/nextflow
@@ -166,8 +166,8 @@ function launch_nextflow() {
     for x in "${launcher[@]}"; do
         x="${x%\"}"
         x="${x#\"}"
-        cmdline+=("$x")
-    done
+        cmdline+=("$x") 
+    done 
 
     if [[ "$bg" ]]; then
       local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
@@ -460,6 +460,7 @@ else
       launcher+=("${cmd_tail[@]}")
     fi
 
+    # create the launch file only when using the legacy launcher (capsule)
     if [[ $NXF_LEGACY_LAUNCHER ]]; then
     # Don't show errors if the LAUNCH_FILE can't be created
     if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then