local IFS=.

local i ver1 ver2

read -r -a ver1 <<< "${1//./ }"

read -r -a ver2 <<< "${2//./ }"

# Compare major, minor, and patch numbers

for ((i=0; i<3; i++)); do

ver1[i]=${ver1[i]//[^0-9]}

ver2[i]=${ver2[i]//[^0-9]}

[[ ${ver1[i]:-0} -lt ${ver2[i]:-0} ]] && echo -1 && return

[[ ${ver1[i]:-0} -gt ${ver2[i]:-0} ]] && echo 1 && return

done

# Extract suffixes for comparison

local suffix1="${1##*.}"

local suffix2="${2##*.}"

suffix1="${suffix1//[0-9]}"

suffix2="${suffix2//[0-9]}"

# Compare suffixes

[[ -z $suffix1 && -n $suffix2 ]] && echo 1 && return

[[ -n $suffix1 && -z $suffix2 ]] && echo -1 && return

[[ $suffix1 < $suffix2 ]] && echo -1 && return

[[ $suffix1 > $suffix2 ]] && echo 1 && return

# Versions are equal

echo 0

if command -v curl &>/dev/null; then

GET="curl -fsSL '$1' -o '$2'"

elif command -v wget &>/dev/null; then

GET="wget '$1' -O '$2' >/dev/null 2>&1"

else

echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"

exit 1

fi

printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. "

eval $GET; status=$?

printf "\r\033[K"

if [ $status -ne 0 ]; then

echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet"

echo ""

echo "Alternatively you can try to download this file:"

echo " $1"

echo ""

echo "and save it as:"

echo " ${3:-$2}"

echo ""

exit 1

fi

if command -v curl &>/dev/null; then

curl -fsSL "$1"

elif command -v wget &>/dev/null; then

wget "$1" >/dev/null 2>&1

else

echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"

exit 1

fi

local base=${NXF_TEMP:=$PWD}

if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $?

else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $?

fi

[[ ! -f $1 ]] && exit 1

if command -v realpath &>/dev/null; then

realpath "$1"

elif command -v readlink &>/dev/null; then

local target="$1"

cd "$(dirname "$target")"; target="$(basename "$target")"

while [ -L "$target" ]; do

target="$(readlink "$target")"

cd "$(dirname "$target")"; target="$(basename "$target")"

done

echo "$(cd "$(dirname "$target")"; pwd -P)/$target"

else

echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found"

exit 1

fi

local tmpfile=$(make_temp)

local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver)

local action="a=${2:-default}"

get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $?

mv "$tmpfile" "$1" || exit $?

chmod +x "$1" || exit $?

bash "$1" -download || exit $?

echo ''

echo -e $'Nextflow installation completed. Please note:'

echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1)

if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then

echo -e $'- you may complete the installation by moving it to a directory in your $PATH'

fi

echo ''

}

function check_latest() {

[[ $cmd != run ]] && return 0

[[ $NXF_OFFLINE == true || $NXF_DISABLE_CHECK_LATEST == true ]] && return 0

local latest=$(get_ver "$NXF_BASE/$(current_ver)/version?current=$NXF_VER")

if [[ -n "$latest" && $(cmp_ver "$latest" "$NXF_VER") -gt 0 ]]; then

echo_yellow "Nextflow $latest is available - Please consider updating your version to it"

fi

}

function launch_nextflow() {

# the launch command line

local cmdline=()

# remove leading and trailing double-quotes

for x in "${launcher[@]}"; do

x="${x%\"}"

x="${x#\"}"

cmdline+=("$x")

done

if [[ "$bg" ]]; then

local pid_file="${NXF_PID_FILE:-.nextflow.pid}"

cmdline+=("${args[@]}")

exec "${cmdline[@]}" &

disown

echo $! > "$pid_file"

exit 0

fi

cmdline+=("${args[@]}")

exec "${cmdline[@]}"

exit 1

}

if [ "$0" = "bash" ] || [[ "$0" =~ .*/bash ]]; then

if [ -d nextflow ]; then

echo 'Please note:'

echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists."

echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder."

echo ''

exit 1

fi

install "$PWD/nextflow" install

exit 0

unset JAVA_TOOL_OPTIONS

bg=''

declare -a jvmopts=()

declare -a args=("$@")

declare -a commands=(clone config drop help history info ls pull run view node console kuberun)

[ "$NXF_CLI_OPTS" ] && args+=($NXF_CLI_OPTS)

cmd=''

while [[ $# != 0 ]]; do

case $1 in

-D*)

if [[ ! "$cmd" ]]; then

jvmopts+=("$1")

fi

;;

-bg)

bg=1

;;

-remote-debug)

echo_yellow "Enabling script debugging - continue the execution launching the remote VM debugger in your favourite IDE using port $NXF_REMOTE_DEBUG_PORT"

remote_debug=1

;;

-download)

if [[ ! "$cmd" ]]; then

rm -rf "$NXF_DIST/$NXF_VER" || exit $?

bash "$0" -version || exit $?

exit 0

fi

;;

-self-update|self-update)

if [[ ! "$cmd" ]]; then

[[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1

unset NXF_VER

install "$0" update

exit 0

fi

;;

*)

[[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1

;;

esac

shift

CAPSULE_LOG=${CAPSULE_LOG:=''}

CAPSULE_RESET=${CAPSULE_RESET:=''}

CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}

NXF_PACK=one

NXF_MODE=${NXF_MODE:-''}

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_HOST=${HOSTNAME:-localhost}

[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST}

NXF_GRAB=${NXF_GRAB:-''}

NXF_CLASSPATH=${NXF_CLASSPATH:-''}

if [[ $NXF_PACK = dist ]]; then

NXF_BIN=$(which "$0" 2>/dev/null)

[ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"

if [[ "$NXF_JAVA_HOME" ]]; then

JAVA_HOME="$NXF_JAVA_HOME"

unset JAVA_CMD

if [ ! -x "$JAVA_CMD" ] ; then

if [ -d "$JAVA_HOME" ] ; then

if [ -x "$JAVA_HOME/jre/sh/java" ] ; then

# IBM's JDK on AIX uses strange locations for the executables

JAVA_CMD="$JAVA_HOME/jre/sh/java"

else

JAVA_CMD="$JAVA_HOME/bin/java"

fi

elif [ -x /usr/libexec/java_home ]; then

JAVA_CMD="$(/usr/libexec/java_home -v 17+ 2>/dev/null)/bin/java" || JAVA_CMD=java

else

JAVA_CMD="$(which java)" || JAVA_CMD=java

fi

JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')"

if [ -f "$JAVA_KEY" ]; then

JAVA_VER="$(cat "$JAVA_KEY")"

JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)"

if [ $? -ne 0 ]; then

getstarted_web="https://www.nextflow.io/docs/latest/getstarted.html"

echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}"

echo_red "NOTE: Nextflow needs a Java virtual machine to run. To this end:

echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n"

exit 1

fi

JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')

# check NF version

if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then

echo_red "Not a valid Nextflow version: $NXF_VER"

exit 1

fi

major=${BASH_REMATCH[1]}

minor=${BASH_REMATCH[2]}

version_check="^(17|18|19|20|21|22|23)"

version_message="Java 17 or later (up to 23)"

if [[ ! $JAVA_VER =~ $version_check ]]; then

echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"

if [[ "$NXF_JAVA_HOME" ]]; then

echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_JAVA_HOME: $NXF_JAVA_HOME\n"

else

echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n JAVA_HOME: $JAVA_HOME\n"

fi

exit 1

fi

mkdir -p "$(dirname "$JAVA_KEY")"

[[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"

if [ ! -f "$NXF_BIN" ]; then

[ -f "$NXF_PATH" ] && rm "$NXF_PATH"

mkdir -p "$NXF_PATH" || exit $?

tmpfile=$(make_temp)

get "$NXF_URL" "$tmpfile" "$NXF_BIN"

mv "$tmpfile" "$NXF_BIN"

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)

if [[ $cmd == console ]]; then bg=1;

else JAVA_OPTS+=(-Djava.awt.headless=true)

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)

[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)

[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)

[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH

[[ "$NXF_GRAB" ]] && export NXF_GRAB

[[ "$COLUMNS" ]] && export COLUMNS

[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$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

export NXF_PACK

export NXF_ENABLE_VIRTUAL_THREADS

if hash md5sum 2>/dev/null; then MD5=md5sum;

elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum;

elif hash md5 2>/dev/null; then MD5=md5;

else MD5=''

if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then

launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))

launch_nextflow

exit 1

env_md5() {

cat <<EOF | $MD5 | cut -f1 -d' '

}

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"))"

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

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 ]]

declare -a cmd_base="(${BASH_REMATCH[1]})"

declare -a cmd_tail="(${BASH_REMATCH[2]})"

launcher="${cmd_base[@]}"

[[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)

[[ "$remote_debug" ]] && launcher+=(-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT)

launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)

launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)

launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)

launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)

launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)

launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)

launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)

launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)

launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)

launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)

if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then

if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)

elif [[ ! "$JAVA_VER" =~ ^(21|22|23) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"

fi

fi

launcher+=("${cmd_tail[@]}")

# 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

STR=''

for x in "${launcher[@]}"; do

[[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+=$(printf '%q ' "$x")

done

printf "$STR">"$LAUNCH_FILE"

else

echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?"

fi

fi

check_latest

launch_nextflow