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Fix errors when NXF_HOME contains spaces #4456

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Merged
pditommaso merged 2 commits into from
Oct 31, 2023
Merged

Fix errors when NXF_HOME contains spaces #4456

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e4868d0
Fix errors when NXF_HOME contains spaces
bentsherman Oct 28, 2023
ba7bd19
Apply suggestions from review
bentsherman Oct 29, 2023
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8 changes: 4 additions & 4 deletions nextflow
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Original file line number Diff line number Diff line change
Expand Up @@ -320,7 +320,7 @@ else
if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21) ]]; then
echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 21\n"
fi
mkdir -p $(dirname "$JAVA_KEY")
mkdir -p "$(dirname "$JAVA_KEY")"
[[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
fi

Expand Down Expand Up @@ -404,8 +404,8 @@ else
# 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]})
cmd_tail=(${BASH_REMATCH[2]})
declare -a cmd_base="(${BASH_REMATCH[1]})"
declare -a cmd_tail="(${BASH_REMATCH[2]})"

launcher="${cmd_base[@]}"
[[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
Expand Down Expand Up @@ -443,7 +443,7 @@ else
if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
STR=''
for x in "${launcher[@]}"; do
[[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+="$x "
[[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+=$(printf '%q ' "$x")
done
printf "$STR">"$LAUNCH_FILE"
else
Expand Down