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Archive old step log files on rerun #32

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3 changes: 3 additions & 0 deletions inst/templates/workflow/SWF/controller.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,9 @@ make_env_cur_vars "$SWF_CUR"
# Run the next sbatch job
if [[ -f "$SWF__JOB_SCRIPT" ]]
then
# Archive old log files for this step before submitting
archive_old_logs "${SWF_NAME}_step${SWF_CUR}" "$SLURM_JOB_ID" "$SWF_LOG_DIR"

sbatch --dependency=afterany:"$SLURM_JOB_ID" \
--output="$SWF__STEPS_OUT" \
--job-name="${SWF_NAME}_step${SWF_CUR}" \
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30 changes: 30 additions & 0 deletions inst/templates/workflow/SWF/lib.sh
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Expand Up @@ -25,6 +25,36 @@ function make_env_cur_vars {
export SWF__INSTRUCTIONS_SCRIPT="$SWF__CUR_DIR/instructions.sh"
}

# Archive old log files for a step before resubmitting it.
# Moves .out files with a job ID lower than the current one to log/archive/.
# Arguments:
# $1 - step name (e.g., "wf_name_step1")
# $2 - current SLURM job ID (files with lower IDs are considered old)
# $3 - log directory path
function archive_old_logs {
local step_name="$1"
local current_jobid="$2"
local log_dir="$3"
local archive_dir="$log_dir/archive"

for f in "$log_dir"/${step_name}_*.out; do
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@AdrienLeGuillou AdrienLeGuillou Mar 6, 2026

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That is not a valid bash line. You can't index out of a glob.
find "$log_dir" -name "${step_name}_*.out" actually list them.
This can be stored in a variable then iterated on

[ -f "$f" ] || continue

local basename
basename=$(basename "$f")
# Remove the step_name_ prefix and .out suffix to get JOBID_TASKID
local remainder="${basename#${step_name}_}"
remainder="${remainder%.out}"
# Extract the job ID (part before the first _)
local file_jobid="${remainder%%_*}"

if [[ "$file_jobid" =~ ^[0-9]+$ ]] && [ "$file_jobid" -lt "$current_jobid" ]; then
mkdir -p "$archive_dir"
mv "$f" "$archive_dir/"
fi
done
}

# convert CRLF endings to LF - `|| echo ""` prevents error when none is found
function fix_crlf_files {
local CRLF_FILES=$(find "$1" -type f | xargs file -F "::" | grep CRLF || echo "")
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