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[Nextflow]: Update trace file configuration #4202

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[Nextflow]: Update trace file configuration #4202

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d49e82b
Create separate nextflow config for execution trace file at $NXF_HOME…
kamyshova Dec 5, 2025
523c910
#4202 cleanup
SilinPavel Dec 5, 2025
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41 changes: 35 additions & 6 deletions deploy/docker/cp-tools/base/nextflow/nextflow
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ function _expand() { eval "echo \"$1\""; }
CP_NF_WORKDIR=$(_expand "${CP_NF_WORKDIR:-${ANALYSIS_DIR}/work}")
CP_NF_CACHEDIR=$(_expand "${CP_NF_CACHEDIR:-${ANALYSIS_DIR}/cache}")
CP_NF_TRACE_FILE=$(_expand "${CP_NF_TRACE_FILE_DIR:-$CP_NF_WORKDIR}/trace.txt")
CP_NF_TRACE_FIELDS="${CP_NF_TRACE_FIELDS:-"task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes"}"
CP_NF_RUNTIME_DATA_SYNC_PERIOD=${CP_NF_RUNTIME_DATA_SYNC_PERIOD:-300}
CP_NF_RUNTIME_DATA_SYNC_BACKOFF_SEC=10
CP_NF_AUTOGENERATE_PARAMETERS_PATH="${CP_NF_AUTOGENERATE_PARAMETERS_PATH:-$SCRIPTS_DIR/cp_params.json}"
Expand All @@ -76,7 +77,13 @@ mkdir -p "$NXF_WORK"

_ARGS=()
_IS_RUN_COMMAND=
for param in "$@"; do
_NEXTFLOW_CONFIGS=
_NEXTFLOW_CONFIG_OPTION="-c"

while [[ $# -gt 0 ]]; do
param="$1"
shift

if [ "$param" == "run" ]; then
_IS_RUN_COMMAND="1"
fi
Expand All @@ -85,6 +92,17 @@ for param in "$@"; do
CP_NF_WEBLOG_HANDLER_CLEANUP_ON_RUN="1"
continue
fi

if [ "$param" == "-c" ] || [ "$param" == "-C" ]; then
value=$1
_NEXTFLOW_CONFIGS="${value}"
if [ "$param" == "-C" ]; then
_NEXTFLOW_CONFIG_OPTION="-C"
fi
shift
continue
fi

_ARGS+=("$param")
done

Expand Down Expand Up @@ -125,10 +143,19 @@ if [ "$_IS_RUN_COMMAND" == "1" ]; then
echo "weblog.enabled = true" >> $NEXTFLOW_CONFIG
echo "weblog.url = 'http://localhost:${CP_NF_WEBLOG_HANDLER_PORT:-8080}/nextflow/event'" >> $NEXTFLOW_CONFIG
if [ -n "$CP_NF_WORKDIR" ]; then
echo "trace.enabled = true" >> $NEXTFLOW_CONFIG
echo "trace.raw = true" >> $NEXTFLOW_CONFIG
echo "trace.file = \"${CP_NF_TRACE_FILE}\"" >> $NEXTFLOW_CONFIG
echo "trace.fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes'" >> $NEXTFLOW_CONFIG
export TRACE_CONFIG="$NXF_HOME/trace.config"
cat > "$TRACE_CONFIG" <<EOF
trace.enabled = true
trace.raw = true
trace.file = "${CP_NF_TRACE_FILE}"
trace.fields = '${CP_NF_TRACE_FIELDS}'
EOF
if [ ! -z "$_NEXTFLOW_CONFIGS" ]; then
_NEXTFLOW_CONFIGS="${_NEXTFLOW_CONFIGS},${TRACE_CONFIG}"
else
_NEXTFLOW_CONFIGS="$TRACE_CONFIG"
fi
echo "[INFO] The Nextflow execution trace file will be created at ${CP_NF_TRACE_FILE}."
fi
fi

Expand All @@ -143,7 +170,9 @@ if [ -f "$NEXTFLOW_CONFIG" ]; then
cat "$NEXTFLOW_CONFIG"
echo
fi
#

# Define final configs configuration (user provided + trace.config if was configured)
_ARGS+=("$_NEXTFLOW_CONFIG_OPTION" "$_NEXTFLOW_CONFIGS")

# Resume parameters
_ARGS+=('-name')
Expand Down