Next flow initial commit

.gitignore

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+.idea/**
+.gradle/**
+.nextflow.log*
+build/**
+out/**

bin/nextflow.sh

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+#!/bin/bash
+
+#
+#  Copyright (c) 2012, the authors.
+#
+#    This file is part of 'Nextflow'.
+#
+#    Nextflow is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    Nextflow is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+#set -e
+#set -u
+#set -o errexit
+
+# the application 'base' folder
+bin_dir=`dirname "$0"`
+bin_dir=`cd "$bin_dir"; pwd`
+base_dir=`dirname $bin_dir`
+
+# define the java env
+java=java
+if test -n "$JAVA_HOME"; then
+	java="$JAVA_HOME/bin/java"
+fi
+
+#
+# Variable definition
+#
+declare -a args=()
+DEBUG=''
+MAIN_CLASS='nextflow.script.CliRunner'
+JVM_ARGS+=" -Djava.net.preferIPv4Stack=true -Djava.awt.headless=true"
+
+#
+# classpath when the application is compiled with gradle
+#
+if [ -e "$base_dir/build/classes/main" ]; then
+  CLASSPATH="$base_dir/build/classes/main"
+  CLASSPATH+=":$base_dir/build/classes/test"
+  CLASSPATH+=":$base_dir/build/resources/main"
+  for file in $base_dir/build/dependency-libs/*.jar; do
+    CLASSPATH+=":$file";
+  done
+
+#
+# deployed application class -- only jar in the libs folder
+#
+#elif [ -e $base_dir/libs ]; then
+#  CLASSPATH="$base_dir/conf"
+#  for file in $base_dir/libs/*.jar; do
+#    CLASSPATH+=":$file";
+#  done
+
+else
+  echo "Missing application libraries -- Nextflow cannot start"
+  exit 1
+fi
+
+
+#
+# Handle special program cli options
+#
+while [ "$*" != "" ]; do
+  if [[ "$1" == '--debug' || "$1" == '--trace' ]]; then
+    args+=("$1")
+
+  elif [ "$1" == '--with-jrebel' ]; then
+    if [ "$JREBEL_HOME" ]; then
+    JVM_ARGS+=" -javaagent:$JREBEL_HOME/jrebel.jar -Drebel.log.file=./jrebel-client.log"
+    else
+    echo "WARN: To use JReber define the JREBEL_HOME variable in environment"
+    fi
+
+  elif [ "$1" == '--remote-debugger' ]; then
+    DEBUG='-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=8010'
+
+  else
+   args+=("$1")
+  fi
+  # move to the next option
+  shift
+done
+
+# Show some variable when in DEBUG mode
+if [ "$DEBUG" != '' ]; then
+  echo Launch environment
+  echo ------------------
+  echo base_dir: $base_dir
+  echo jvmargs: $JVM_ARGS
+  echo debug: $DEBUG
+  echo classpath:
+  echo $CLASSPATH | tr ":" "\n" | sort
+  echo ''
+  echo Launching it!
+  echo ------------------
+fi
+
+# Launch the APP
+exec java $JVM_ARGS $DEBUG -cp "$CLASSPATH" "$MAIN_CLASS" "${args[@]}"

build.gradle

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+/*
+ * Copyright (c) 2012, the authors.
+ *
+ *   This file is part of 'Nextflow'.
+ *
+ *   Nextflow is free software: you can redistribute it and/or modify
+ *   it under the terms of the GNU General Public License as published by
+ *   the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   Nextflow is distributed in the hope that it will be useful,
+ *   but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *   GNU General Public License for more details.
+ *
+ *   You should have received a copy of the GNU General Public License
+ *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+apply plugin: 'groovy'
+version = '0.1'
+status = 'alpha'
+
+repositories {
+    flatDir(dirs: file('lib'))
+    mavenCentral()
+}
+
+dependencies {
+
+    groovy module ('org.codehaus.groovy:groovy-all:2.1.1') {
+        transitive = true
+    }
+
+    compile (
+            'org.codehaus.gpars:gpars:1.0.0',
+            'org.slf4j:slf4j-api:1.7.2',
+            'org.slf4j:jcl-over-slf4j:1.7.2',
+            'org.slf4j:jul-to-slf4j:1.7.2',
+            'org.slf4j:log4j-over-slf4j:1.7.2',
+            'ch.qos.logback:logback-classic:1.0.9',
+            'ch.qos.logback:logback-core:1.0.9',
+            'commons-lang:commons-lang:2.6',
+            'commons-io:commons-io:2.4',
+            'com.google.guava:guava:13.0.1',
+            'com.beust:jcommander:1.30',
+            'jline:jline:2.9',
+            'org.fusesource.jansi:jansi:1.9'
+    )
+
+    testCompile ('org.spockframework:spock-core:0.7-groovy-2.0')
+
+}
+
+
+
+/*
+ * print out the runtime classpath
+ */
+task classpathRuntime(dependsOn: configurations.runtime) << {
+
+    String home = System.properties['user.home']
+    def libs = configurations.compile.collect {File file -> file.absolutePath ?.replace(home,'$HOME')}
+    println libs.join(':')
+
+}
+
+/*
+ * print out the compile classpath
+ */
+task classpathCompile(dependsOn: configurations.compile) << {
+
+    String home = System.properties['user.home']
+    def libs = configurations.compile.collect {File file -> file.absolutePath ?.replace(home,'$HOME')}
+    println libs.join(':')
+
+}
+
+
+/*
+ * Update the build timestamp in the source source file
+ */
+task buildInfo << {
+
+    def file = new File('./src/main/groovy/nextflow/Const.groovy')
+    def buildNum = 0
+    def src = file.text
+    src.find(/APP_BUILDNUM *= *([0-9]*)/) { buildNum = it[1]?.toInteger()+1 }
+    src = src.replaceAll('APP_VER *= *"[0-9\\.]+"', "APP_VER = \"${version}\"" as String)
+    src = src.replaceAll('APP_TIMESTAMP *= *[0-9]*', "APP_TIMESTAMP = ${System.currentTimeMillis()}" as String)
+    if( buildNum ) {
+        src = src.replaceAll('APP_BUILDNUM *= *[0-9]*', "APP_BUILDNUM = ${buildNum}" as String)
+    }
+    else {
+        println "WARN: Unable to find current build number"
+    }
+    file.text = src
+
+
+}
+
+/*
+ * Compile sources and copies all libs to target directory
+ */
+task compile(type: Copy) {
+    dependsOn buildInfo, compileJava, compileGroovy, processResources
+
+    into "$buildDir/dependency-libs"
+    from configurations.runtime
+}
+
+
+/*
+ * Create the distribution stage folder i.e. creates a folder containing everythinh
+ * have to be included in the distribution package
+ */
+
+task stage( type: Copy ) {
+    dependsOn jar, javadoc, groovydoc
+
+    // clean the target directory before create
+    def target = file("$buildDir/stage/nextflow-$version")
+    target.parentFile.deleteDir()
+    target.mkdirs()
+
+    destinationDir target
+
+//    // copy the bin scripts
+//    into('bin') {
+//        from ('./bin') { exclude 'circo' }
+//        rename { String fileName -> fileName.replace('circo.sh', 'circo') }
+//    }
+
+    // copy application - and - runtime dependencies jars
+    into('libs') {
+        from "$buildDir/libs/nextflow-${version}.jar"
+        from configurations.runtime
+    }
+
+    // still some stuff
+    into('conf') { from './src/main/resources' }
+    into('src') { from './src/main' }
+    into('docs') { from '$buildDir/docs/groovydoc/'}
+
+}
+
+/*
+ * Creates the Zip distribution file
+ */
+task distZip(type: Zip) {
+    dependsOn stage
+    from "$buildDir/stage/"
+}
+
+/*
+ * creates the Tar distribution file
+ */
+task distTar(type: Tar) {
+    dependsOn stage
+    compression = Compression.GZIP
+    from "$buildDir/stage/"
+}
+
+task dist() {
+    dependsOn distZip, distTar
+}
+
+/*
+ * Print the distribution file name when distXxx task completes
+ */
+gradle.taskGraph.afterTask { Task task, TaskState state ->
+    if (task == distTar && !state.failure) { println "\n** TAR: ${relativePath(distTar.archivePath)}\n\n"}
+    if (task == distZip && !state.failure) { println "\n** ZIP: ${relativePath(distZip.archivePath)}\n\n"}
+}

examples/blast.nextflow

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+def fasta='/Users/ptommaso/sample.fa'
+def DB='/Users/ptommaso/tools/blast-db/pdb/pdb'
+
+def sequences = task('split') {
+
+    input fasta:[fasta]
+    output 'seq_*'
+
+        """
+        gcsplit $fasta '%^>%' '/^>/' '{*}' -f seq_
+        """
+}
+
+
+def singleBlast = task('blast') {
+
+    input seq: sequences
+    output 'blast_result'
+
+        """
+        blastp -db $DB -query $seq -outfmt 6 > blast_result
+        """
+
+}
+
+
+def allBlast = merge {
+
+    input blast:singleBlast
+    output 'allBlast'
+
+        """
+        cat $blast >> allBlast
+        """
+
+}
+
+def result = task('sort') {
+    input result:allBlast
+        """
+        sort $result
+        """
+}
+
+
+println read(result)

examples/env.nextflow

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+env [ 'HELLO' ]  = '1'
+
+task {
+    echo true
+    "env | sort"
+}
+

examples/hello.nextflow

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+task {
+    """
+    echo 'Hello world'
+    """
+}

examples/vars.nextflow

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+x = 1
+def y = 2
+
+println "x: $x"
+println "y: $y"
+println "z: $z"

nextflow.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src/main/groovy" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/groovy" isTestSource="true" />
+      <excludeFolder url="file://$MODULE_DIR$/build" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" exported="" name="jsr166y-1.7.0" level="project" />
+    <orderEntry type="library" exported="" name="gpars-1.0.0" level="project" />
+    <orderEntry type="library" exported="" name="logback-classic-1.0.9" level="project" />
+    <orderEntry type="library" exported="" name="commons-lang-2.6" level="project" />
+    <orderEntry type="library" exported="" name="jline-2.9" level="project" />
+    <orderEntry type="library" exported="" name="jul-to-slf4j-1.7.2" level="project" />
+    <orderEntry type="library" exported="" name="groovy-all-2.1.1" level="project" />
+    <orderEntry type="library" exported="" name="jansi-1.9" level="project" />
+    <orderEntry type="library" exported="" name="jcl-over-slf4j-1.7.2" level="project" />
+    <orderEntry type="library" exported="" name="slf4j-api-1.7.2" level="project" />
+    <orderEntry type="library" scope="TEST" name="junit-dep-4.10" level="project" />
+    <orderEntry type="library" exported="" name="log4j-over-slf4j-1.7.2" level="project" />
+    <orderEntry type="library" exported="" name="guava-13.0.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="hamcrest-core-1.3" level="project" />
+    <orderEntry type="library" exported="" name="logback-core-1.0.9" level="project" />
+    <orderEntry type="library" scope="TEST" name="spock-core-0.7-groovy-2.0" level="project" />
+    <orderEntry type="library" exported="" name="jcommander-1.30" level="project" />
+    <orderEntry type="library" exported="" name="commons-io-2.4" level="project" />
+  </component>
+</module>
+