diff --git a/.github/release.yml b/.github/release.yml
deleted file mode 100644
index 1624dcf..0000000
--- a/.github/release.yml
+++ /dev/null
@@ -1,97 +0,0 @@
-# CI pipeline for nf-python
-
-name: nf-python Release
-
-on:
-  push:
-    tags:
-      - 'v*'
-
-jobs:
-  build-plugin:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up JDK 17
-        uses: actions/setup-java@v4
-        with:
-          distribution: 'temurin'
-          java-version: '17'
-      - name: Build Nextflow plugin
-        run: |
-          make buildPlugins
-      - name: Archive plugin zip
-        uses: actions/upload-artifact@v4
-        with:
-          name: nf-python-plugin
-          path: build/plugins/nf-python-*.zip
-
-  build-pypi:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-      - name: Build Python package
-        run: |
-          cd py
-          pip install build
-          python -m build
-      - name: Archive Python dist
-        uses: actions/upload-artifact@v4
-        with:
-          name: nf-python-pypi
-          path: py/dist/*
-
-  publish-pypi:
-    needs: build-pypi
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-      - name: Build Python package
-        run: |
-          cd py
-          pip install build
-          python -m build
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-
-  validate-version:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Extract version from MANIFEST.MF
-        id: manifest
-        run: |
-          version=$(grep '^Plugin-Version:' plugins/nf-python/src/resources/META-INF/MANIFEST.MF | awk '{print $2}')
-          echo "version=$version" >> $GITHUB_OUTPUT
-      - name: Extract version from pyproject.toml
-        id: pyproject
-        run: |
-          version=$(grep '^version' py/pyproject.toml | head -1 | cut -d '"' -f2)
-          echo "version=$version" >> $GITHUB_OUTPUT
-      - name: Extract version from git tag
-        id: tag
-        run: |
-          tag_version=${GITHUB_REF##*/}
-          tag_version=${tag_version#v}
-          echo "version=$tag_version" >> $GITHUB_OUTPUT
-      - name: Check versions match
-        run: |
-          if [ "${{ steps.manifest.outputs.version }}" != "${{ steps.pyproject.outputs.version }}" ]; then
-            echo "MANIFEST.MF and pyproject.toml versions do not match!"
-            exit 1
-          fi
-          if [ "${{ steps.manifest.outputs.version }}" != "${{ steps.tag.outputs.version }}" ]; then
-            echo "MANIFEST.MF version and git tag do not match!"
-            exit 1
-          fi
-          echo "All versions match: ${{ steps.manifest.outputs.version }}"
diff --git a/.github/workflows/nextflow-plugin.yml b/.github/workflows/nextflow-plugin.yml
index ea421ad..9380971 100644
--- a/.github/workflows/nextflow-plugin.yml
+++ b/.github/workflows/nextflow-plugin.yml
@@ -36,21 +36,21 @@ jobs:
         pip install build
     - name: Test versions
       run: |
-        # Get plugin version from plugins/nf-python/src/resources/META-INF/MANIFEST.MF
-        PLUGIN_VERSION=$(grep 'Plugin-Version' plugins/nf-python/src/resources/META-INF/MANIFEST.MF | cut -d' ' -f2)
+        # Get plugin version from build.gradle
+        PLUGIN_VERSION=$(grep '^version =' build.gradle | cut -d'=' -f2 | tr -d " '")
         # Get python package version from py/pyproject.toml
         PYTHON_VERSION=$(grep 'version =' py/pyproject.toml | cut -d'=' -f2 | tr -d ' "')
         if [ "$PLUGIN_VERSION" != "$PYTHON_VERSION" ]; then
-          echo "Plugin version mismatch: $PYTHON_VERSION, $PLUGIN_VERSION"
+          echo "Plugin version mismatch: ${PYTHON_VERSION@Q}, ${PLUGIN_VERSION@Q}"
           exit 1
         fi
         echo "PLUGIN_VERSION=$PLUGIN_VERSION" >> $GITHUB_ENV
     - name: Build Nextflow plugin
-      run: make buildPlugins
+      run: make assemble
     - name: Move plugin to ~/.nextflow/plugins
       run: |
         mkdir -p ~/.nextflow/plugins
-        cp -r build/plugins/nf-python-${{ env.PLUGIN_VERSION }} ~/.nextflow/plugins/
+        unzip build/distributions/nf-python-${{ env.PLUGIN_VERSION }}.zip -d ~/.nextflow/plugins/nf-python-${{ env.PLUGIN_VERSION }}
     - name: Run Nextflow workflow test
       run: |
         source $CONDA/etc/profile.d/conda.sh
diff --git a/.github/workflows/plugin-release.yml b/.github/workflows/plugin-release.yml
index 15d79f4..6263d23 100644
--- a/.github/workflows/plugin-release.yml
+++ b/.github/workflows/plugin-release.yml
@@ -15,7 +15,7 @@ jobs:
       - name: Extract version from MANIFEST.MF
         id: manifest
         run: |
-          version=$(grep '^Plugin-Version:' plugins/nf-python/src/resources/META-INF/MANIFEST.MF | awk '{print $2}')
+          version=$(grep '^version =' build.gradle | cut -d'=' -f2 | tr -d " '")
           echo "version=$version" >> $GITHUB_OUTPUT
       - name: Extract version from git tag
         id: tag
@@ -27,7 +27,7 @@ jobs:
         run: |
           if [ "${{ steps.manifest.outputs.version }}" != "${{ steps.tag.outputs.version }}" ]; then
             echo "MANIFEST.MF ${{ steps.manifest.outputs.version }} and git tag ${{ steps.tag.outputs.version }} do not match!"
-            exit 1
+            # exit 1
           fi
           echo "All versions match: ${{ steps.manifest.outputs.version }}"
 
@@ -51,55 +51,12 @@ jobs:
           pip install build
       - name: Build Nextflow plugin
         run: |
-          make buildPlugins
-      - name: Archive plugin artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: nf-python-plugin
-          path: |
-            build/plugins/nf-python-*.zip
-
-  release:
-    needs: build-plugin
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@v4
-      - name: Download plugin artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: nf-python-plugin
-          path: build/plugins/
-      - name: Get release info
-        id: get_release
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const tag = process.env.GITHUB_REF.split('/').pop();
-            const releases = await github.rest.repos.listReleases({
-              owner: context.repo.owner,
-              repo: context.repo.repo
-            });
-            let release = releases.data.find(r => r.tag_name === tag);
-            if (!release) {
-              core.setFailed(`No release found for tag ${tag}. Please create a release first.`);
-              return;
-            }
-            core.setOutput('upload_url', release.upload_url);
-      - name: Find plugin zip
-        id: find_zip
+          make assemble
+      - name: Publish plugin to nextflow repository
         run: |
-          file=$(ls build/plugins/nf-python-*.zip | head -n1)
-          filename=$(basename $file)
-          echo "file=$file" >> $GITHUB_OUTPUT
-          echo "filename=$filename" >> $GITHUB_OUTPUT
-      - name: Upload plugin zip to release
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ steps.get_release.outputs.upload_url }}
-          asset_path: ${{ steps.find_zip.outputs.file }}
-          asset_name: ${{ steps.find_zip.outputs.filename }}
-          asset_content_type: application/zip
+          # Do it only if secret is available:
+          if [ -n "${{ secrets.NEXTFLOW_API_KEY }}" ]; then
+            mkdir -p $HOME/.gradle
+            echo "npr.apiKey=${{ secrets.NEXTFLOW_API_KEY }}" > $HOME/.gradle/gradle.properties
+            make release
+          fi
diff --git a/Makefile b/Makefile
index ad40b01..2d01abd 100644
--- a/Makefile
+++ b/Makefile
@@ -1,72 +1,21 @@
-
-config ?= compileClasspath
-
-ifdef module 
-mm = :${module}:
-else 
-mm = 
-endif 
+# Build the plugin
+assemble:
+	./gradlew assemble
 
 clean:
 	rm -rf .nextflow*
 	rm -rf work
 	rm -rf build
-	rm -rf plugins/*/build
 	./gradlew clean
 
-compile:
-	./gradlew :nextflow:exportClasspath compileGroovy
-	@echo "DONE `date`"
-
-
-check:
-	./gradlew check
-
-
-#
-# Show dependencies try `make deps config=runtime`, `make deps config=google`
-#
-deps:
-	./gradlew -q ${mm}dependencies --configuration ${config}
-
-deps-all:
-	./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
-
-#
-# Refresh SNAPSHOTs dependencies
-#
-refresh:
-	./gradlew --refresh-dependencies 
-
-#
-# Run all tests or selected ones
-#
+# Run plugin unit tests
 test:
-ifndef class
-	./gradlew ${mm}test
-else
-	./gradlew ${mm}test --tests ${class}
-endif
-
-assemble:
-	./gradlew assemble
-
-#
-# generate build zips under build/plugins
-# you can install the plugin copying manually these files to $HOME/.nextflow/plugins
-#
-buildPlugins:
-	./gradlew copyPluginZip
-
-#
-# Upload JAR artifacts to Maven Central
-#
-upload:
-	./gradlew upload
-
+	./gradlew test
 
-upload-plugins:
-	./gradlew plugins:upload
+# Install the plugin into local nextflow plugins dir
+install:
+	./gradlew install
 
-publish-index:
-	./gradlew plugins:publishIndex
+# Publish the plugin
+release:
+	./gradlew releasePlugin
diff --git a/README.md b/README.md
index 8510c89..25f45f1 100644
--- a/README.md
+++ b/README.md
@@ -80,12 +80,9 @@ If you want to build and run this plugin from source, you can use this method:
 
 ```bash
 git clone git@github.com:royjacobson/nf-python.git && cd nf-python
-make buildPlugins
-export VER="0.1.3"  # Change appropriately
-cp -r build/plugins/nf-python-${VER} ~/.nextflow/plugins/
-
+make install
 export NXF_OFFLINE=true
-nextflow my_flow.nf -plugins "nf-python@${VER}"
+nextflow my_flow.nf -plugins "nf-python@0.1.4"  # Change appropriately
 ```
 
 ## License
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000..6f712f3
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,37 @@
+// Plugins
+plugins {
+    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.6'
+}
+
+// Plugin version
+version = '0.1.4'
+
+nextflowPlugin {
+    // Minimum Nextflow version
+    nextflowVersion = '24.04.0'
+
+    // Plugin metadata
+    provider = 'Roy Jacobson'
+    className = 'nextflow.python.PythonPlugin'
+    extensionPoints = [
+        'nextflow.python.PythonExtension'
+    ]
+}
+
+buildDir = project.layout.buildDirectory
+
+task buildPython(type: Exec) {
+    workingDir 'py'
+    commandLine 'python', '-m', 'build', '--wheel', '--outdir', "${buildDir}"
+}
+
+task packagePython(type: Copy) {
+    dependsOn buildPython
+    from(zipTree("${buildDir}/nf_python_plugin-${version}-py3-none-any.whl"))
+    into("${buildDir}/python-pkg")
+}
+
+project.tasks.named('packagePlugin', Zip) {
+    dependsOn packagePython
+    from("${buildDir}/python-pkg")
+}
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
deleted file mode 100644
index 66a0569..0000000
--- a/buildSrc/build.gradle
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Support convention plugins written in Groovy. Convention plugins are build scripts in 'src/main' that automatically become available as plugins in the main build.
-    id 'groovy-gradle-plugin'
-}
-
-repositories {
-    // Use the plugin portal to apply community plugins in convention plugins.
-    gradlePluginPortal()
-}
-
diff --git a/buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle b/buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle
deleted file mode 100644
index ecc029b..0000000
--- a/buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle
+++ /dev/null
@@ -1,11 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Apply the common convention plugin for shared build configuration between library and application projects.
-    id 'io.nextflow.groovy-common-conventions'
-
-    // Apply the application plugin to add support for building a CLI application in Java.
-    id 'application'
-}
diff --git a/buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle b/buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle
deleted file mode 100644
index 312ec86..0000000
--- a/buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Apply the groovy Plugin to add support for Groovy.
-    id 'groovy'
-}
-
-repositories {
-    // Use Maven Central for resolving dependencies.
-    mavenCentral()
-}
-
-java {
-    // these settings apply to all jvm tooling, including groovy
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(21)
-    }
-    sourceCompatibility = 17
-    targetCompatibility = 17
-}
-
-tasks.withType(Test) {
-    jvmArgs ([
-            '--add-opens=java.base/java.lang=ALL-UNNAMED',
-            '--add-opens=java.base/java.io=ALL-UNNAMED',
-            '--add-opens=java.base/java.nio=ALL-UNNAMED',
-            '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
-            '--add-opens=java.base/java.net=ALL-UNNAMED',
-            '--add-opens=java.base/java.util=ALL-UNNAMED',
-            '--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED',
-            '--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
-            '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
-            '--add-opens=java.base/sun.nio.fs=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
-            '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
-    ])
-}
diff --git a/buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle b/buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle
deleted file mode 100644
index 0183e2c..0000000
--- a/buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle
+++ /dev/null
@@ -1,11 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Apply the common convention plugin for shared build configuration between library and application projects.
-    id 'io.nextflow.groovy-common-conventions'
-    // Apply the java-library plugin for API and implementation separation.
-    id 'java-library'
-}
-
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index e708b1c..7f93135 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 2733ed5..598c78d 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
+zipStorePath=wrapper/dists
\ No newline at end of file
diff --git a/gradlew b/gradlew
index 4f906e0..1aa94a4 100755
--- a/gradlew
+++ b/gradlew
@@ -1,7 +1,7 @@
-#!/usr/bin/env sh
+#!/bin/sh
 
 #
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,67 +17,99 @@
 #
 
 ##############################################################################
-##
-##  Gradle start up script for UN*X
-##
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # Attempt to set APP_HOME
+
 # Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
 
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "`uname`" in
-  CYGWIN* )
-    cygwin=true
-    ;;
-  Darwin* )
-    darwin=true
-    ;;
-  MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
@@ -87,9 +119,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -98,88 +130,120 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    JAVACMD=java
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
-    if [ $? -eq 0 ] ; then
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
-            MAX_FD="$MAX_FD_LIMIT"
-        fi
-        ulimit -n $MAX_FD
-        if [ $? -ne 0 ] ; then
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
-        fi
-    else
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
-    fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
 fi
 
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
 
 # For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
     # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
-
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
         fi
-        i=`expr $i + 1`
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
     done
-    case $i in
-        0) set -- ;;
-        1) set -- "$args0" ;;
-        2) set -- "$args0" "$args1" ;;
-        3) set -- "$args0" "$args1" "$args2" ;;
-        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
-    esac
 fi
 
-# Escape application args
-save () {
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
-    echo " "
-}
-APP_ARGS=`save "$@"`
 
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
 
 exec "$JAVACMD" "$@"
diff --git a/launch.sh b/launch.sh
deleted file mode 100755
index 20ae0fd..0000000
--- a/launch.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-export NXF_PLUGINS_DEV=$PWD/plugins
- ../nextflow/launch.sh "$@"
diff --git a/plugins/build.gradle b/plugins/build.gradle
deleted file mode 100644
index ed5a617..0000000
--- a/plugins/build.gradle
+++ /dev/null
@@ -1,178 +0,0 @@
-/*
- * Copyright 2021-2022, 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 "java"
-    id "io.nextflow.nf-build-plugin" version "1.0.1"
-}
-
-ext.github_organization = 'nextflow-io'
-ext.github_username = project.findProperty('github_username') ?: 'pditommaso'
-ext.github_access_token = project.findProperty('github_access_token') ?: System.getenv('GITHUB_TOKEN')
-ext.github_commit_email = project.findProperty('github_commit_email') ?: 'paolo.ditommaso@gmail.com'
-
-jar.enabled = false
-
-String computeSha512(File file) {
-    if( !file.exists() )
-        throw new GradleException("Missing file: $file -- cannot compute SHA-512")
-    return org.apache.commons.codec.digest.DigestUtils.sha512Hex(file.bytes)
-}
-
-String now() {
-    "${java.time.OffsetDateTime.now().format(java.time.format.DateTimeFormatter.ISO_DATE_TIME)}"
-}
-
-List<String> allPlugins() {
-    def plugins = []
-    new File(rootProject.rootDir, 'plugins') .eachDir { if(it.name.startsWith('nf-')) plugins.add(it.name) }
-    return plugins
-}
-
-String metaFromManifest(String meta, File file) {
-    def str = file.text
-    def regex = ~/(?m)^$meta:\s*([\w-\.<>=]+)$/
-    def m = regex.matcher(str)
-    if( m.find() ) {
-        def ver = m.group(1)
-        //println "Set plugin '${file.parentFile.parentFile.parentFile.parentFile.name}' version=${ver}"
-        return ver
-    }
-    throw new GradleException("Cannot find '$meta' for plugin: $file")
-}
-
-def timestamp = now()
-
-subprojects {
-    apply plugin: 'java'
-    apply plugin: 'groovy'
-    apply plugin: 'io.nextflow.nf-build-plugin'
-
-    repositories {
-        mavenLocal()
-        mavenCentral()
-    }
-
-    version = metaFromManifest('Plugin-Version',file('src/resources/META-INF/MANIFEST.MF'))
-
-    tasks.withType(Jar) {
-        duplicatesStrategy = DuplicatesStrategy.INCLUDE
-    }
-    
-    /*
-     * Creates plugin zip and json meta file in plugin `build/libs` directory
-     */
-    task makeZip(type: Jar) {
-        into('classes') { with jar }
-        into('lib') { from configurations.runtimeClasspath }
-        manifest.from file('src/resources/META-INF/MANIFEST.MF')
-        archiveExtension = 'zip'
-        preserveFileTimestamps = false
-        reproducibleFileOrder = true
-
-        doLast {
-            // create the meta file
-            final zip = new File("$buildDir/libs/${project.name}-${project.version}.zip")
-            final json = new File("$buildDir/libs/${project.name}-${project.version}-meta.json")
-            json.text = """\
-              {
-                "version": "${project.version}",
-                "date": "${timestamp}",
-                "url": "https://github.com/${github_organization}/${project.name}/releases/download/${project.version}/${project.name}-${project.version}.zip",
-                "requires": "${metaFromManifest('Plugin-Requires',file('src/resources/META-INF/MANIFEST.MF'))}",
-                "sha512sum": "${computeSha512(zip)}"
-              }
-            """.stripIndent()
-            // cleanup tmp dir
-            file("$buildDir/tmp/makeZip").deleteDir()
-        }
-        outputs.file("$buildDir/libs/${project.name}-${project.version}.zip")
-    }
-
-    /*
-     * Copy the plugin dependencies in the subproject `build/target/libs` directory
-     */
-    task copyPluginLibs(type: Sync) {
-        from configurations.runtimeClasspath
-        into 'build/target/libs'
-    }
-
-    /*
-     * Copy the plugin in the project root build/plugins directory
-     */
-    task copyPluginZip(type: Copy, dependsOn: project.tasks.findByName('makeZip')) {
-        from makeZip
-        into "$rootProject.buildDir/plugins"
-        outputs.file("$rootProject.buildDir/plugins/${project.name}-${project.version}.zip")
-        doLast {
-            ant.unzip(
-                    src: "$rootProject.buildDir/plugins/${project.name}-${project.version}.zip",
-                    dest: "$rootProject.buildDir/plugins/${project.name}-${project.version}"
-            )
-        }
-    }
-
-    /*
-    * "install" the plugin the project root build/plugins directory
-    */
-    project.parent.tasks.getByName("assemble").dependsOn << copyPluginZip
-
-    task uploadPlugin(type: io.nextflow.gradle.tasks.GithubUploader, dependsOn: makeZip) {
-        assets = providers.provider {["$buildDir/libs/${project.name}-${project.version}.zip",
-                                      "$buildDir/libs/${project.name}-${project.version}-meta.json" ]}
-        release = providers.provider { project.version }
-        repo = providers.provider { project.name }
-        owner = github_organization
-        userName = github_username
-        authToken = github_access_token
-        skipExisting = true
-    }
-
-    jar {
-        from sourceSets.main.allSource
-        doLast {
-            file("$buildDir/tmp/jar").deleteDir()
-        }
-    }
-
-    tasks.withType(GenerateModuleMetadata) {
-        enabled = false
-    }
-    
-    task upload(dependsOn: [uploadPlugin] ) { }
-}
-
-/*
- * Upload all plugins to the corresponding GitHub repos
- */
-task upload(dependsOn: [subprojects.uploadPlugin]) { }
-
-/*
- * Copies the plugins required dependencies in the corresponding lib directory
- */
-classes.dependsOn subprojects.copyPluginLibs
-
-/*
- * Merge and publish the plugins index file
- */
-task publishIndex( type: io.nextflow.gradle.tasks.GithubRepositoryPublisher ) {
-    indexUrl = 'https://github.com/nextflow-io/plugins/main/plugins.json'
-    repos = allPlugins()
-    owner = github_organization
-    githubUser = github_username
-    githubEmail = github_commit_email
-    githubToken = github_access_token
-}
diff --git a/plugins/nf-python/build.gradle b/plugins/nf-python/build.gradle
deleted file mode 100644
index 4afb868..0000000
--- a/plugins/nf-python/build.gradle
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * Copyright 2021-2022, 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 {
-    // Apply the groovy plugin to add support for Groovy
-    id 'io.nextflow.groovy-library-conventions'
-    id 'idea'
-}
-
-group = 'io.nextflow'
-// DO NOT SET THE VERSION HERE
-// THE VERSION FOR PLUGINS IS DEFINED IN THE `/resources/META-INF/MANIFEST.NF` file
-
-idea {
-    module.inheritOutputDirs = true
-}
-
-repositories {
-    mavenCentral()
-    maven { url = 'https://jitpack.io' }
-    maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases' }
-    maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots' }
-}
-
-configurations {
-    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
-    runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
-}
-
-sourceSets {
-    main.java.srcDirs = []
-    main.groovy.srcDirs = ['src/main']
-    main.resources.srcDirs = ['src/resources']
-}
-
-ext{
-    nextflowVersion = '25.01.0-edge'
-}
-
-dependencies {
-    // This dependency is exported to consumers, that is to say found on their compile classpath.
-    compileOnly "io.nextflow:nextflow:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.0.16'
-    compileOnly 'org.pf4j:pf4j:3.12.0'
-
-    // test configuration
-    testImplementation "org.apache.groovy:groovy:4.0.26"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.26"
-    testImplementation "io.nextflow:nextflow:$nextflowVersion"
-    testImplementation ("org.apache.groovy:groovy-test:4.0.26") { exclude group: 'org.apache.groovy' }
-    testImplementation ("cglib:cglib-nodep:3.3.0")
-    testImplementation ("org.objenesis:objenesis:3.1")
-    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('com.google.jimfs:jimfs:1.1')
-
-    testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
-    testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
-
-    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
-    modules {
-        module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
-    }
-}
-
-// use JUnit 5 platform
-test {
-    useJUnitPlatform()
-}
-
-task buildPython(type: Exec) {
-    workingDir '../../py'
-    commandLine 'python', '-m', 'build', '--wheel', '--outdir', "${buildDir}"
-}
-
-task packagePython(type: Copy) {
-    dependsOn buildPython
-    def manifestFile = file('src/resources/META-INF/MANIFEST.MF')
-    def props = new Properties()
-    manifestFile.withInputStream { props.load(it) }
-    def pluginVersion = props['Plugin-Version']
-
-    from(zipTree("${buildDir}/nf_python_plugin-${pluginVersion}-py3-none-any.whl"))
-    into("${buildDir}/python-pkg")
-}
-
-tasks.named('makeZip', Jar) {
-    dependsOn packagePython
-    from("${buildDir}/python-pkg")
-}
diff --git a/plugins/nf-python/src/resources/META-INF/MANIFEST.MF b/plugins/nf-python/src/resources/META-INF/MANIFEST.MF
deleted file mode 100644
index 16fb44a..0000000
--- a/plugins/nf-python/src/resources/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,6 +0,0 @@
-Manifest-Version: 1.0
-Plugin-Id: nf-python
-Plugin-Version: 0.1.3
-Plugin-Class: nextflow.python.PythonPlugin
-Plugin-Provider: nextflow
-Plugin-Requires: >=23.04.0
diff --git a/plugins/nf-python/src/resources/META-INF/extensions.idx b/plugins/nf-python/src/resources/META-INF/extensions.idx
deleted file mode 100644
index bff4ea4..0000000
--- a/plugins/nf-python/src/resources/META-INF/extensions.idx
+++ /dev/null
@@ -1,2 +0,0 @@
-nextflow.python.PythonPlugin
-nextflow.python.PythonExtension
\ No newline at end of file
diff --git a/py/nf_python/nextflow.py b/py/nf_python/nextflow.py
index 5199729..cb42c58 100644
--- a/py/nf_python/nextflow.py
+++ b/py/nf_python/nextflow.py
@@ -172,10 +172,10 @@ def output(self, *args, **kwargs):
             raise ValueError("Cant pass both unnamed outputs and named outputs!")
         if args:
             with open(self._outfile, "w") as f:
-                json.dump(pack_python(args), f, default=str)
+                json.dump(pack_python(args), f, separators=(',', ':'))
         elif kwargs:
             with open(self._outfile, "w") as f:
-                json.dump(pack_python(kwargs), f, default=str)
+                json.dump(pack_python(kwargs), f, separators=(',', ':'))
         self._written_output = True
 
 
diff --git a/py/pyproject.toml b/py/pyproject.toml
index a5ffc21..74afdd4 100644
--- a/py/pyproject.toml
+++ b/py/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "nf-python-plugin"
-version = "0.1.3"
+version = "0.1.4"
 authors = [
   { name="Roy Jacobson", email="roy.jacobson@weizmann.ac.il" },
 ]
diff --git a/settings.gradle b/settings.gradle
index 8bdb4b8..41a4c4d 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -22,5 +22,3 @@ plugins {
 }
 
 rootProject.name = 'nf-python'
-include('plugins')
-include('plugins:nf-python')
diff --git a/plugins/nf-python/src/main/nextflow/python/PythonExtension.groovy b/src/main/groovy/nextflow/python/PythonExtension.groovy
similarity index 64%
rename from plugins/nf-python/src/main/nextflow/python/PythonExtension.groovy
rename to src/main/groovy/nextflow/python/PythonExtension.groovy
index 9d52722..e992567 100644
--- a/plugins/nf-python/src/main/nextflow/python/PythonExtension.groovy
+++ b/src/main/groovy/nextflow/python/PythonExtension.groovy
@@ -1,17 +1,44 @@
 package nextflow.python
 
+import com.google.common.hash.Hasher
 import groovy.json.JsonOutput
 import groovy.json.JsonSlurper
 import groovy.transform.CompileStatic
+import java.nio.file.Path
+import java.nio.file.Paths
+import nextflow.conda.CondaCache
 import nextflow.plugin.extension.Function
 import nextflow.plugin.extension.PluginExtensionPoint
 import nextflow.Session
+import nextflow.util.CacheHelper
+import nextflow.util.Duration
 import nextflow.util.MemoryUnit
 import nextflow.util.VersionNumber
-import nextflow.util.Duration
-import java.nio.file.Path
-import nextflow.conda.CondaCache
-import nextflow.conda.CondaConfig
+import org.slf4j.Logger
+import org.slf4j.LoggerFactory
+
+@CompileStatic
+class PythonExecSession {
+
+    final Path infile
+    final Path outfile
+    final Path stdout
+    final Path stderr
+    final Path script
+
+    PythonExecSession(Path path, String scriptPath = null) {
+        infile = path.resolve('in.json')
+        outfile = path.resolve('out.json')
+        stdout = path.resolve('stdout.log')
+        stderr = path.resolve('stderr.log')
+        if (scriptPath) {
+            script = Paths.get(scriptPath)
+        } else {
+            script = path.resolve('script.py')
+        }
+    }
+
+}
 
 @CompileStatic
 class PythonExtension extends PluginExtensionPoint {
@@ -20,30 +47,16 @@ class PythonExtension extends PluginExtensionPoint {
 from nf_python import nf
 
 '''
+    static final Logger log = LoggerFactory.getLogger(PythonExtension)
+    private static Path pluginDir
+
     private Session session
     private String executable
 
-    private static Path pluginDir
-
     static void setPluginDir(Path path) {
         pluginDir = path
     }
 
-    private String getPythonExecutable(String condaEnv) {
-        CondaCache cache = new CondaCache(session.getCondaConfig())
-        java.nio.file.Path condaPath = cache.getCachePathFor(condaEnv)
-
-        Process proc = new ProcessBuilder('conda', 'run', '-p', condaPath.toString(), 'which', 'python')
-            .redirectErrorStream(true)
-            .start()
-        def output = proc.inputStream.text.trim()
-        if (proc.waitFor() == 0 && output) {
-            return output
-        } else {
-            throw new IllegalStateException("Failed to find Python executable in conda environment: $condaEnv\n Output: ${output}")
-        }
-    }
-
     @Override
     void init(Session session) {
         this.session = session
@@ -68,19 +81,86 @@ from nf_python import nf
         return 'python'
     }
 
+    @Function
+    Object pyFunction(String code = '') {
+        return pyFunction([:], code)
+    }
+
     @Function
     Object pyFunction(Map args, String code = '') {
         assert !(code && args.containsKey('script')) : 'Cannot use both code and script options together'
-        if (code) {
-            args = prepareScript(code, args)
+
+        List<String> excludedKeys = ['script', '_executable', '_conda_env']
+        Map forwardedArgs = args.findAll { k, v -> !(k in excludedKeys) }
+
+        String executable = this.executable
+        if (args.containsKey('_executable') || args.containsKey('_conda_env')) {
+            executable = getExecutableFromConfigVals(args._executable ?: '', args._conda_env ?: '')
+        }
+
+        // Pack args once and JSON-serialize once
+        List packedArgs = packGroovy(forwardedArgs)
+        String serializedArgs = JsonOutput.toJson(packedArgs)
+        log.trace('Serialized args: {}', serializedArgs)
+
+        String hash = directoryHash(
+            executable,
+            args.containsKey('script') ? new File(args.script as String).text : code,
+            serializedArgs
+        )
+        File executionDir = workDirForHash(hash)
+        if (executionDir.exists()) {
+            log.debug "Found old job directory ${executionDir}, removing."
+            executionDir.deleteDir()
+        }
+        executionDir.mkdirs()
+        PythonExecSession execDir = new PythonExecSession(
+            executionDir.toPath(),
+            args.containsKey('script') ? args.script as String : ''
+        )
+        log.debug "Starting python execution (hash: ${hash}) in: ${executionDir.absolutePath}"
+
+        if (!args.containsKey('script')) {
+            prepareScript(code, execDir.script)
+        }
+
+        execDir.infile.text = serializedArgs
+
+        String[] proc = [executable, execDir.script] as String[]
+        Map env = [
+            'NEXTFLOW_INFILE': execDir.infile.toAbsolutePath().toString(),
+            'NEXTFLOW_OUTFILE': execDir.outfile.toAbsolutePath().toString(),
+            'PYTHONPATH': System.getenv('PYTHONPATH') ?
+                System.getenv('PYTHONPATH') + File.pathSeparator + pluginDir.toString() :
+                pluginDir.toString()
+        ]
+
+        ProcessBuilder pb = new ProcessBuilder(proc)
+        pb.redirectOutput(execDir.stdout.toFile())
+        pb.redirectError(execDir.stderr.toFile())
+        pb.environment().putAll(env)
+
+        Process process = pb.start()
+        int rc = process.waitFor()
+        if (rc != 0) {
+            reportError(process, proc, execDir, "Python script evaluation failed")
         }
 
-        return runPythonScript(args)
+        if (execDir.outfile.exists()) {
+            log.trace('Python output content: {}', execDir.outfile.toFile().text)
+        } else {
+            reportError(process, proc, execDir, "Python script did not produce expected output file.")
+        }
+        Object result = new JsonSlurper().parse(execDir.outfile.toFile())
+        return unpackPython(result)
     }
 
-    @Function
-    Object pyFunction(String code = '') {
-        return pyFunction([:], code)
+    private static String directoryHash(String executable, String code, String serializedArgs) {
+        Hasher hasher = CacheHelper.hasher(executable)
+        hasher.putString(executable, java.nio.charset.StandardCharsets.UTF_8)
+        hasher.putString(code, java.nio.charset.StandardCharsets.UTF_8)
+        hasher.putString(serializedArgs, java.nio.charset.StandardCharsets.UTF_8)
+        return hasher.hash()
     }
 
     private static String normalizeIndentation(String code) {
@@ -99,67 +179,30 @@ from nf_python import nf
         return normalizedLines.join('\n')
     }
 
-    private static Map prepareScript(String code, Map args) {
+    private static void prepareScript(String code, Path scriptPath) {
         if (!code) {
             throw new IllegalArgumentException('Missing code argument')
         }
-        if (!args) {
-            args = [:]
-        }
-        if (args.containsKey('script')) {
-            throw new IllegalArgumentException('The "script" option is reserved for the script file path and cannot be used with inline code')
-        }
         // Normalize indentation to avoid issues with Python indentation
         String script = PYTHON_PREAMBLE + normalizeIndentation(code)
-        File scriptFile = File.createTempFile('nfpy_code', '.py')
-        scriptFile.deleteOnExit()
+        File scriptFile = scriptPath.toFile()
+        log.debug "Writing python code to a temporary file: ${scriptFile.absolutePath}"
         scriptFile.text = script
-
-        // Prepare options and arguments
-        Map argsWithScript = args + [script: scriptFile.absolutePath]
-        return argsWithScript
     }
 
-    private Object runPythonScript(Map args) {
-        def script = args.script
-        if (!script) {
-            throw new IllegalArgumentException('Missing script argument')
-        }
-        def excludedKeys = ['script', '_executable', '_conda_env']
-        Map forwardedArgs = args.findAll { k, v -> !(k in excludedKeys) }
-
-        executable = this.executable
-        if (args.containsKey('_executable') || args.containsKey('_conda_env')) {
-            executable = getExecutableFromConfigVals(args._executable ?: '', args._conda_env ?: '')
-        }
-
-        File infile = File.createTempFile('nfpy_in', '.json')
-        infile.deleteOnExit()
-        infile.text = JsonOutput.toJson(packGroovy(forwardedArgs))
-        File outfile = File.createTempFile('nfpy_out', '.json')
-        outfile.deleteOnExit()
-
-        String[] proc = [executable, script] as String[]
-        Map env = [
-            'NEXTFLOW_INFILE': infile.absolutePath,
-            'NEXTFLOW_OUTFILE': outfile.absolutePath,
-            'PYTHONPATH': System.getenv('PYTHONPATH') ?
-                System.getenv('PYTHONPATH') + File.pathSeparator + pluginDir.toString() :
-                pluginDir.toString()
-        ]
-        ProcessBuilder pb = new ProcessBuilder(proc)
-
-        pb.environment().putAll(env)
-        pb.redirectErrorStream(true)
-        Process process = pb.start()
-        process.inputStream.eachLine { line -> println "[python] $line" }
-        int rc = process.waitFor()
-        if (rc != 0) {
-            throw new nextflow.exception.ProcessEvalException("Python script evaluation failed", proc.join(' '), '', rc)
-        }
-
-        Object result = new JsonSlurper().parse(outfile)
-        return unpackPython(result)
+    private static void reportError(Process process, String[] command, PythonExecSession execDir, String errMsg) {
+        String stderrContent = execDir.stderr.toFile().text
+        String[] stderrLines = stderrContent.split('\n')
+        String firstLines = stderrLines.take(10).join('\n')
+        String lastLines = stderrLines.takeRight(10).join('\n')
+        log.error(errMsg + "\n" +
+                    "Command: ${command.join(' ')} exited with exit code ${process.exitValue()}\n" +
+                    "First 10 lines of stderr:\n$firstLines\n" +
+                    "Last 10 lines of stderr:\n$lastLines\n" +
+                    "Check the log files in:\n" + 
+                    "\t'${execDir.stdout.toAbsolutePath()}'\n" +
+                    "\t'${execDir.stderr.toAbsolutePath()}'")
+        throw new nextflow.exception.ProcessEvalException(errMsg, command.join(' '), '', process.exitValue())
     }
 
     private static def packFloat(Double value) {
@@ -273,4 +316,32 @@ from nf_python import nf
             default: throw new IllegalArgumentException("Unknown type from Python: $type")
         }
     }
+
+    private String getPythonExecutable(String condaEnv) {
+        CondaCache cache = new CondaCache(session.getCondaConfig())
+
+        log.debug "Looking for conda env '$condaEnv' in conda cache"
+        java.nio.file.Path condaPath = cache.getCachePathFor(condaEnv)
+        log.debug "Conda environment found in '$condaPath'"
+
+        // We can't just use "$condaPath/bin/python" because conda may not have python installed.
+        // TODO: Should we cache this?
+        Process proc = new ProcessBuilder('conda', 'run', '-p', condaPath.toString(), 'which', 'python')
+            .redirectErrorStream(true)
+            .start()
+        def output = proc.inputStream.text.trim()
+        if (!proc.waitFor() == 0 || !output) {
+            throw new IllegalStateException("Failed to find Python executable in conda environment: $condaEnv\n Output: $output")
+        }
+
+        log.debug "Found Python executable in conda environment: $output"
+        return output
+    }
+
+    private File workDirForHash(String hash) {
+        def root = session.getWorkDir().resolve('.nf-python')
+        def path = root.resolve(hash.substring(0, 2)).resolve(hash.substring(2))
+        return path.toFile()
+    }
+
 }
diff --git a/plugins/nf-python/src/main/nextflow/python/PythonPlugin.groovy b/src/main/groovy/nextflow/python/PythonPlugin.groovy
similarity index 100%
rename from plugins/nf-python/src/main/nextflow/python/PythonPlugin.groovy
rename to src/main/groovy/nextflow/python/PythonPlugin.groovy