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Log run metadata to a shared directory #97

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Log run metadata to a shared directory #97

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96b8314
feat(metrics): dump run metadata metrics to shared directory for late…
nbtm-sh Jun 5, 2026
2c51111
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jscgh Jun 9, 2026
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25 changes: 25 additions & 0 deletions template/script.sh.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ DB_PATH=${DB_PATH:-/srv/scratch/sbf-pipelines/proteinfold/dbs}
BRANCH=${BRANCH:-v2.0.0}
REPOSITORY=${REPOSITORY:-nf-core/proteinfold}
DEBUGGROUP=${DEBUGGROUP:-sbf}
METRICS_DIRECTORY=${METRICS_DIRECTORY:-/srv/scratch/sbf-pipelines/metrics}
ENABLE_METRICS=${ENABLE_METRICS:-true}

set -xo pipefail
set -eE
Expand Down Expand Up @@ -340,6 +342,29 @@ if [ "${SAVE_INTERMEDIATES}" == "true" ]; then
ARGS="${ARGS} --save_intermediates true"
fi

if [[ "${ENABLE_METRICS}" == "true" ]]; then
# Write metrics before starting the run Create yyyy/mm directory to avoid large file count in one directory and to make collecting metrics by month easier.
METRICS_LOG_PATH="${METRICS_DIRECTORY}/$(date +%Y/%m)"
mkdir -p "${METRICS_LOG_PATH}"

# Write json file containing job metrics.
NF_CONFIG="${NEXTFLOW_CONFIG_ARGS[@]}"
jq -n \
--arg date "$(date +%Y-%m-%dT%H:%M:%SZ%z)" \
--arg user "$(whoami)" \
--arg node "$(hostname)" \
--arg pbs_jobid "${PBS_JOBID}" \
--arg mode "${PROT_MODE}" \
--arg repository "${REPOSITORY}" \
--arg branch "${BRANCH}" \
--arg input "${SAMPLESHEET}" \
--arg outdir "${OUT_DIR}" \
--arg nf_config "${NF_CONFIG}" \
--arg args "${ARGS}" \
'{date: $date, user: $user, node: $node, pbs_jobid: $pbs_jobid, mode: $mode, repository: $repository, branch: $branch, input: $input, outdir: $outdir, nf_config: $nf_config, args: $args}' > "${METRICS_LOG_PATH}/$(date +%Y-%m-%dT%H:%M:%SZ%z)-$(whoami)-${PBS_JOBID%.*}.json"

fi

nextflow "${NEXTFLOW_CONFIG_ARGS[@]}" run ${REPOSITORY} -r ${BRANCH} -latest \
--input "${SAMPLESHEET}" \
--outdir "${OUT_DIR}" \
Expand Down
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