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add telemetry to reconstructr
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dpark01 committed Dec 19, 2023
1 parent c4f319c commit 9bedb51
Showing 1 changed file with 11 additions and 3 deletions.
14 changes: 11 additions & 3 deletions pipes/WDL/tasks/tasks_interhost.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -574,12 +574,20 @@ task reconstructr {
# compress outputs
pigz -9 -p $(nproc) "~{out_basename}-tabulate.tsv" "~{out_basename}-decipher.tsv" "~{out_basename}-states.Rdata"
# profiling and stats
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
output {
File tabulated_tsv_gz = "~{out_basename}-tabulate.tsv.gz"
File deciphered_tsv_gz = "~{out_basename}-decipher.tsv.gz"
File mcmc_states_Rdata_gz = "~{out_basename}-states.Rdata.gz"
File tabulated_tsv_gz = "~{out_basename}-tabulate.tsv.gz"
File deciphered_tsv_gz = "~{out_basename}-decipher.tsv.gz"
File mcmc_states_Rdata_gz = "~{out_basename}-states.Rdata.gz"
Int max_ram_gb = ceil(read_float("MEM_BYTES")/1000000000)
Int runtime_sec = ceil(read_float("UPTIME_SEC"))
String cpu_load = read_string("CPU_LOAD")
}
runtime {
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