#!/bin/bash
### ---
### name: 'SOMATIC_CNV_REF_BUILDER:SOMA_CNV_BUILD_REFERENCE (build_reference)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-3cb5ec5'
### outputs:
### - 'batch_reference.parquet'
### - 'sex_calls.csv'
### - 'feature_stats.csv'
### - 'versions.yml'
### ...
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}
nxf_tree() {
local pid=$1
declare -a ALL_CHILDREN
while read P PP;do
ALL_CHILDREN[$PP]+=" $P"
done < <(ps -e -o pid= -o ppid=)
pstat() {
local x_pid=$1
local STATUS=$(2> /dev/null < /proc/$1/status grep -E 'Vm|ctxt')
if [ $? = 0 ]; then
local x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
local x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
local x_peak=$(echo "$STATUS" | grep -E 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
cpu_stat[x_pid]="$x_pid $x_pmem $x_vsz $x_rss $x_peak $vol_ctxt $inv_ctxt"
fi
}
pwalk() {
pstat $1
for i in ${ALL_CHILDREN[$1]:=}; do pwalk $i; done
}
pwalk $1
}
nxf_stat() {
cpu_stat=()
nxf_tree $1
declare -a sum=(0 0 0 0 0 0 0 0)
local pid
local i
for pid in "${!cpu_stat[@]}"; do
local row=(${cpu_stat[pid]})
[ $NXF_DEBUG = 1 ] && echo "++ stat mem=${row[*]}"
for i in "${!row[@]}"; do
if [ $i != 0 ]; then
sum[i]=$((sum[i]+row[i]))
fi
done
done
[ $NXF_DEBUG = 1 ] && echo -e "++ stat SUM=${sum[*]}"
for i in {1..7}; do
if [ ${sum[i]} -lt ${cpu_peak[i]} ]; then
sum[i]=${cpu_peak[i]}
else
cpu_peak[i]=${sum[i]}
fi
done
[ $NXF_DEBUG = 1 ] && echo -e "++ stat PEAK=${sum[*]}\n"
nxf_stat_ret=(${sum[*]})
}
nxf_mem_watch() {
set -o pipefail
local pid=$1
local trace_file=.command.trace
local count=0;
declare -a cpu_stat=(0 0 0 0 0 0 0 0)
declare -a cpu_peak=(0 0 0 0 0 0 0 0)
local mem_tot=$(< /proc/meminfo grep MemTotal | awk '{print $2}')
local timeout
local DONE
local STOP=''
[ $NXF_DEBUG = 1 ] && nxf_sleep 0.2 && ps fx
while true; do
nxf_stat $pid
if [ $count -lt 10 ]; then timeout=1;
elif [ $count -lt 120 ]; then timeout=5;
else timeout=30;
fi
read -t $timeout -r DONE || true
[[ $DONE ]] && break
if [ ! -e /proc/$pid ]; then
[ ! $STOP ] && STOP=$(nxf_date)
[ $(($(nxf_date)-STOP)) -gt 10000 ] && break
fi
count=$((count+1))
done
printf "%s\n" \
"%mem=${nxf_stat_ret[1]}" \
"vmem=${nxf_stat_ret[2]}" \
"rss=${nxf_stat_ret[3]}" \
"peak_vmem=${nxf_stat_ret[4]}" \
"peak_rss=${nxf_stat_ret[5]}" \
"vol_ctxt=${nxf_stat_ret[6]}" \
"inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
}
nxf_write_trace() {
printf "%s\n" \
"nextflow.trace/v2" \
"realtime=$wall_time" \
"%cpu=$ucpu" \
"cpu_model=$cpu_model" \
"rchar=${io_stat1[0]}" \
"wchar=${io_stat1[1]}" \
"syscr=${io_stat1[2]}" \
"syscw=${io_stat1[3]}" \
"read_bytes=${io_stat1[4]}" \
"write_bytes=${io_stat1[5]}" >| "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
}
nxf_trace_mac() {
local start_millis=$(nxf_date)
/bin/bash -Ceuo pipefail .command.sh
local end_millis=$(nxf_date)
local wall_time=$((end_millis-start_millis))
local ucpu=''
local cpu_model=''
local io_stat1=('' '' '' '' '' '')
nxf_write_trace
}
nxf_fd() {
local FD=11
while [ -e /proc/$$/fd/$FD ]; do FD=$((FD+1)); done
echo $FD
}
nxf_trace_linux() {
local pid=$$
command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; }
local num_cpus=$(< /proc/cpuinfo grep '^processor' -c)
local cpu_model=$(< /proc/cpuinfo grep '^model name' | head -n 1 | awk 'BEGIN{FS="\t: "} { print $2 }')
local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
local start_millis=$(nxf_date)
trap 'kill $mem_proc' ERR
/bin/bash -Ceuo pipefail .command.sh &
local task=$!
mem_fd=$(nxf_fd)
eval "exec $mem_fd> >(nxf_mem_watch $task)"
local mem_proc=$!
wait $task
local end_millis=$(nxf_date)
local tot_time1=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
local cpu_time1=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
local ucpu=$(awk -v p1=$cpu_time1 -v p0=$cpu_time0 -v t1=$tot_time1 -v t0=$tot_time0 -v n=$num_cpus 'BEGIN { pct=(p1-p0)/(t1-t0)*100*n; printf("%.0f", pct>0 ? pct : 0) }' )
local io_stat1=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
local i
for i in {0..5}; do
io_stat1[i]=$((io_stat1[i]-io_stat0[i]))
done
local wall_time=$((end_millis-start_millis))
[ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"
printf "%s\n" \
"nextflow.trace/v2" \
"realtime=$wall_time" \
"%cpu=$ucpu" \
"cpu_model=$cpu_model" \
"rchar=${io_stat1[0]}" \
"wchar=${io_stat1[1]}" \
"syscr=${io_stat1[2]}" \
"syscw=${io_stat1[3]}" \
"read_bytes=${io_stat1[4]}" \
"write_bytes=${io_stat1[5]}" >| "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
[ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true
wait $mem_proc 2>/dev/null || true
while [ -e /proc/$mem_proc ]; do nxf_sleep 0.1; done
}
nxf_trace() {
local trace_file=.command.trace
touch $trace_file
if [[ $(uname) = Darwin ]]; then
nxf_trace_mac
else
nxf_trace_linux
fi
}
# bash helper functions
nxf_cp_retry() {
local max_attempts=1
local timeout=10
local attempt=0
local exitCode=0
while (( $attempt < $max_attempts ))
do
if "$@"
then
return 0
else
exitCode=$?
fi
if [[ $exitCode == 0 ]]
then
break
fi
nxf_sleep $timeout
attempt=$(( attempt + 1 ))
timeout=$(( timeout * 2 ))
done
}
nxf_parallel() {
IFS=$'\n'
local cmd=("$@")
local cpus=$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
local max=$(if (( cpus>4 )); then echo 4; else echo $cpus; fi)
local i=0
local pid=()
(
set +u
while ((i<${#cmd[@]})); do
local copy=()
for x in "${pid[@]}"; do
# if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
# see https://github.com/nextflow-io/nextflow/pull/4050
[[ -e /proc/$x ]] && copy+=($x) || wait $x
done
pid=("${copy[@]}")
if ((${#pid[@]}>=$max)); then
nxf_sleep 0.2
else
eval "${cmd[$i]}" &
pid+=($!)
((i+=1))
fi
done
for p in "${pid[@]}"; do
wait $p
done
)
unset IFS
}
# aws helper for s5cmd
nxf_s3_upload() {
local name=$1
local s3path=$2
if [[ "$name" == - ]]; then
local tmp=$(nxf_mktemp)
cp /dev/stdin $tmp/$name
/opt/s5cmd/bin/s5cmd --log error cp --storage-class STANDARD $tmp/$name "$s3path"
elif [[ -d "$name" ]]; then
/opt/s5cmd/bin/s5cmd --log error cp --storage-class STANDARD "$name/" "$s3path/$name/"
else
/opt/s5cmd/bin/s5cmd --log error cp --storage-class STANDARD "$name" "$s3path/$name"
fi
}
nxf_s3_download() {
local source=$1
local target=$2
echo " Downloading: $source"
local file_name=$(basename $1)
local is_dir=$(/opt/s5cmd/bin/s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
if [[ $is_dir == 1 ]]; then
/opt/s5cmd/bin/s5cmd --log error cp "$source/*" "$target"
else
/opt/s5cmd/bin/s5cmd --log error cp "$source" "$target"
fi
}
nxf_sleep() {
sleep $1 2>/dev/null || sleep 1;
}
nxf_date() {
local ts=$(date +%s%3N);
if [[ ${#ts} == 10 ]]; then echo ${ts}000
elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
elif [[ ${#ts} == 13 ]]; then echo $ts
else echo "Unexpected timestamp value: $ts"; exit 1
fi
}
nxf_env() {
echo '============= task environment ============='
env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
echo '============= task output =================='
}
nxf_kill() {
declare -a children
while read P PP;do
children[$PP]+=" $P"
done < <(ps -e -o pid= -o ppid=)
kill_all() {
[[ $1 != $$ ]] && kill $1 2>/dev/null || true
for i in ${children[$1]:=}; do kill_all $i; done
}
kill_all $1
}
nxf_mktemp() {
local base=${1:-/tmp}
mkdir -p "$base"
if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
fi
}
nxf_fs_copy() {
local source=$1
local target=$2
local basedir=$(dirname $1)
mkdir -p $target/$basedir
cp -fRL $source $target/$basedir
}
nxf_fs_move() {
local source=$1
local target=$2
local basedir=$(dirname $1)
mkdir -p $target/$basedir
mv -f $source $target/$basedir
}
nxf_fs_rsync() {
rsync -rRl $1 $2
}
nxf_fs_rclone() {
rclone copyto $1 $2/$1
}
nxf_fs_fcp() {
fcp $1 $2/$1
}
on_exit() {
local last_err=$?
local exit_status=${nxf_main_ret:=0}
[[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
[[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
printf -- $exit_status | nxf_s3_upload - s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693/.exitcode || true
set +u
rm -rf $NXF_SCRATCH || true
exit $exit_status
}
on_term() {
set +e
[[ "$pid" ]] && nxf_kill $pid
}
nxf_launch() {
/bin/bash -Ceuo pipefail .command.run nxf_trace
}
nxf_stage() {
true
# stage input files
downloads=(true)
rm -f 869_VJZ-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_G71-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_WKU-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_CXK-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_LT1-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_FHY-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_UPJ-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_ZEN-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_VH9-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_K08-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_OLD-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_Q74-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_VH9-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_XNF-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_WNV-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_OLD-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_W5A-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_CXK-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_34-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_5Z-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_LVG-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_Y7T-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_LT1-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_VJZ-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_FHY-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_K08-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_W5A-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_DFS-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_UPJ-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_G71-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_W5A-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_5Z-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_CXK-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_34-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_G71-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_SPC-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_TWH-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f manifest.tsv
rm -f 869_WKU-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_X9Y-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_FGH-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f .command.run
rm -f 869_Y7T-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_XNF-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_UPJ-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_SPC-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_DFS-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_WKU-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f .command.sh
rm -f 869_VJZ-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_FGH-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_LT1-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_LVG-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_TWH-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_5Z-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_X9Y-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_DFS-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_SPC-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_34-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_Q74-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_WNV-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_VH9-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_OLD-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_ZEN-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_FHY-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_LVG-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_K08-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_FGH-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_ZEN-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_WNV-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_XNF-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz
rm -f 869_Q74-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz
rm -f 869_Y7T-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
rm -f 869_TWH-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/6fb866e48bb864476c6b7b163464d2/869_VJZ-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_VJZ-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/14400ddf6c4f7a1b208f75154aad49/869_G71-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_G71-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/76e7424a80ae052985dccbb34eebe8/869_WKU-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_WKU-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/4b04bd10b7d5b3a56b3770d5f33dd3/869_CXK-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_CXK-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/58448386a01518ff7855c342f1d7c4/869_LT1-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_LT1-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c677c727132205665acb2dc6feab7f/869_FHY-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_FHY-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/fb19f0fd39ddab4ffd42a0325a40cd/869_UPJ-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_UPJ-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/1a7cf86d405d7c8aaecf42bf83ff75/869_ZEN-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_ZEN-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/e371f7b2079035c5704802e42707f5/869_VH9-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_VH9-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/5f9edf3621830b6d8bf61ef8394bdc/869_K08-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_K08-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/58f21207868bbdc7fe18076d91cea6/869_OLD-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_OLD-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/121fe2170c744dca28148463a237c8/869_Q74-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_Q74-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/26fe5be11466675f3a73de5e975a36/869_VH9-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_VH9-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c4e3920b151ccb9697118be46f46e7/869_XNF-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_XNF-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/a5b3474b079bc6b51b5a17c1a0acd1/869_WNV-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_WNV-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/7f7f958f5f9fe7be394cebc0189f23/869_OLD-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_OLD-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/8836d6a8e4380e4f6dff13818c8e60/869_W5A-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_W5A-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/33d436cb0b4626b87c27425a5ee7ce/869_CXK-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_CXK-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/68bd5a0b2c994f323fd1fc8f771502/869_34-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_34-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/2c713ec56285caff580206982777d5/869_5Z-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_5Z-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/ce7277d3eb1877e6b57c60a4b06ded/869_LVG-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_LVG-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/2acf94515f414c536200409cafd97f/869_Y7T-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_Y7T-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3f7857cf3631691670402b25e041e8/869_LT1-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_LT1-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/34d9093726393536d3413eabfe65e6/869_VJZ-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_VJZ-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/0b0a7c636023b97bfb60fed97de414/869_FHY-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_FHY-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/5985d35a8d9ff70a2cc9c26efaeca0/869_K08-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_K08-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/594c81058cc5ec7255a95e29813b62/869_W5A-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_W5A-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/71884357c7efece8be583598c9d107/869_DFS-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_DFS-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/1f9a6e1a43bb82c9ad0aafb259aa8d/869_UPJ-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_UPJ-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/cede6bddf2764c04a1744cc4b64116/869_G71-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_G71-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/cbba3edc8e06c8d9556d1cf4177ecf/869_W5A-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_W5A-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/a6d548a3270de2a7296ac630e27b7a/869_5Z-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_5Z-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0b75551f8743e695c45e8ce453eac9/869_CXK-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_CXK-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/a1c2fd3fc3894f676994d75372d0c1/869_34-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_34-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/9cc11c27d33253468f16bd53309b53/869_G71-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_G71-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/8c0896f57a684ba7af611296ca3243/869_SPC-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_SPC-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/8bcbb3e9efa429c20ec009266dbba7/869_TWH-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_TWH-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/13/f541716778d797b021720dee165e9c/manifest.tsv manifest.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/1b22f1ab3de1b55a6feac950abb413/869_WKU-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_WKU-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/0e84c30e5993ddc44bdc3438b57578/869_X9Y-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_X9Y-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/60b0e3056145d820c27d8ffdc6af7f/869_FGH-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_FGH-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/caaa28af588dc05451adc46b3252e1/869_Y7T-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_Y7T-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/94396672bf60d1959b849b0fad7595/869_XNF-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_XNF-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/ef1463dea2e945950052846b2901c7/869_UPJ-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_UPJ-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/9135c197914be051d8be605ecf5b62/869_SPC-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_SPC-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/1c795f4cd0e5068a74f80a05c0598b/869_DFS-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_DFS-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/b65efd6b146227cf5be5f81d22ab4b/869_WKU-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_WKU-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/510ab02c21dbfbac52c3e6566f44e8/869_VJZ-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_VJZ-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/e0f71ba8540c1ed6ba10e4c0d453e3/869_FGH-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_FGH-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/a74acfa37fc546ed85a859a7424bcc/869_LT1-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_LT1-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/903417715551ca47381202bbcf4b6e/869_LVG-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_LVG-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/e70ea37f8c234fb845313f7259e239/869_TWH-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_TWH-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/8764e8fde77b562157ba272e052e57/869_5Z-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_5Z-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/f5f4653c0de6ffefee013e033ce8c4/869_X9Y-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_X9Y-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/c438dfa55ba3af7edeb04a669ae53b/869_DFS-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_DFS-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/fe4986fd6dadc1dddbd1c79b4a0711/869_SPC-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_SPC-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/935a3a709b71a39180031306f290dc/869_34-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_34-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/f846bf39bafd59dcbec00e14742a06/869_Q74-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_Q74-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/217529695e6298eafcf9b53dc22ec8/869_WNV-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_WNV-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3fe3a44b53f2053f97a945b7611f8e/869_VH9-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_VH9-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/02fa233e2ccee76a17b7369049e352/869_OLD-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_OLD-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/6648e89453c0df80dba56e1c8db506/869_ZEN-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_ZEN-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/6fd6ee8274f1f45568f6a8bdff3e19/869_FHY-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_FHY-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/4b333830e6d52085795bc8fb6f0fff/869_LVG-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_LVG-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/7b446904575fa335891f73f433a77d/869_K08-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_K08-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/e93c92416d5f1de9037dee4ab63a2f/869_FGH-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_FGH-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/a3c6795e729f73bba0b023af0e6322/869_ZEN-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_ZEN-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/010c2839e2876f59fd920fac377dd8/869_WNV-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_WNV-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/a3275cebf253f43fbb661c865cc9e9/869_XNF-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz 869_XNF-N1-BDNA-1_B2377KTLT3_3_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/5e4c364c31ba175c4903359ba9e19c/869_Q74-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz 869_Q74-N1-BDNA-1_B2377KTLT3_2_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d3f0bfef6abe577a3b31731b631536/869_Y7T-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_Y7T-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/fb6174aa43430e705ca27358ed779d/869_TWH-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz 869_TWH-N1-BDNA-1_B2377KTLT3_1_probes.tsv.gz")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (74 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d batch_reference.parquet sex_calls.csv feature_stats.csv versions.yml" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693 || true
}
nxf_unstage() {
if [[ ${nxf_main_ret:=0} == 0 ]]; then
(set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
nxf_unstage_ret=$?
fi
nxf_unstage_controls
}
nxf_main() {
trap on_exit EXIT
trap on_term TERM INT USR2
trap '' USR1
[[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR"
NXF_SCRATCH="$(set +u; nxf_mktemp /tmp)"
[[ $NXF_DEBUG > 0 ]] && nxf_env
echo start | nxf_s3_upload - s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3d1e500f1e2ad481faf9be5afc4693/.command.begin
set +u
set -u
[[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
export NXF_TASK_WORKDIR="$PWD"
nxf_stage
set +e
(set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) &
pid=$!
wait $pid || nxf_main_ret=$?
nxf_unstage
}
$NXF_ENTRY