#!/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/d3/6a4b0522d4b4ade1064bcfe3c1afe5/.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 1029_BPLF-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BA0-N2-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_EDH-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BIHC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_H6Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_032-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BG5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_5O3-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_FR4-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_GGQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BSOQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BGMF-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BSZ8-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_FOO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BOHJ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_5IX-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_I78-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_GS7-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BN9Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BF2U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_FBB-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_HN2-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_8OI-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_3N0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_G5I-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BNG8-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BQMQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BLH5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BOSD-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_EM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_I2U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_0DT-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_I2R-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BSWE-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BK2H-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_GW0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_0NX-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_56D-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_1H5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BICA-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f manifest.tsv
rm -f 1029_05O-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_E36-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_GZP-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f .command.run
rm -f 1029_BDOZ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_FXQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_I5W-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BGFD-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_8AV-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_DV0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_7Y1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BBS1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_3OH-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BCTO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BO4Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_H0U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_C35-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_H7F-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f .command.sh
rm -f 1029_BIHO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BQXQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_4J3-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BRTT-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BQD7-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_I8V-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_G94-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BFKM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BS78-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BQKE-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_I0S-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BBCQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_8BO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_4Z2-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_H0A-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_H5S-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BP21-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BLU1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BBOC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BCB6-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_FWL-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_HX6-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_2IN-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_EFW-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_EMM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_1G0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_HT5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_2LI-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_BJH0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_DOC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
rm -f 1029_H3R-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/548f2df0e0ed57f99451f552e13fa8/1029_BPLF-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BPLF-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/ea3096c779420a32a0ffe6b9389991/1029_BA0-N2-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BA0-N2-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/0d6ada5d3ea4a82d54df63729a328e/1029_EDH-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_EDH-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/5e5ff6ee7ca01a6c74625bf1893557/1029_BIHC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BIHC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/6222c9a224ef8e12b7848ba3191f01/1029_H6Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_H6Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/c6b0c0a34ec4c57f0c7d45ab219792/1029_032-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_032-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/0d1db559db9cf4c792fdf3f0385eab/1029_BG5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BG5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/e33d62673538a9e6420ca0073f8ab3/1029_5O3-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_5O3-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/54d29d926c4542acb9444134371e8f/1029_FR4-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_FR4-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/4db9ffc8950ac996c1cde5a42d67e7/1029_GGQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_GGQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/68e22f037a19b8cffbaa38c75be7a4/1029_BSOQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BSOQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/3e2cb98cc1eccafae7f52fa10e73f0/1029_BGMF-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BGMF-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/ab549426bd0e137268d92b9ccf9eb3/1029_BSZ8-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BSZ8-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/7aa318e7eae3df8e3c102432e06d6b/1029_FOO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_FOO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/c8a8ed641554963f45ad92e8f144f6/1029_BOHJ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BOHJ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/bb835785a9dca9d89905076ec654b4/1029_5IX-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_5IX-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/dbc9c831f2438262a1bc8e715b1890/1029_I78-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_I78-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/492ea742492c4ed09e5fbc56d65832/1029_GS7-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_GS7-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/29cb48332ef38958ad87dd0f5aca2b/1029_BN9Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BN9Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/336e55a6108e16340ade24cbdf5436/1029_BF2U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BF2U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/a055e695853424dc0e7f003ca93ee2/1029_FBB-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_FBB-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/e864c2b0c44e1f9c81fa25ef950f9d/1029_HN2-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_HN2-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/e92019165c210983cf4f3e5b098acc/1029_8OI-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_8OI-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/8565cffd3dd65089122899c47d602c/1029_3N0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_3N0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/ccb5144d45adb0a1c4b93db2655e22/1029_G5I-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_G5I-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/5412fc348b5e42de4c23aaaf68dfcf/1029_BNG8-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BNG8-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/eaab78ee36536ba4a35145dc1b87c7/1029_BQMQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BQMQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/f37be22660de3f0fca3fe5aba630cf/1029_BLH5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BLH5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/52b8dcd973addebd55940a5bdc4a9a/1029_BOSD-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BOSD-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/02d5b778a5b89d8e06ea2c86068010/1029_EM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_EM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/d2e12d976447515499777818ccbec9/1029_I2U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_I2U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e039989c4b5811fba2141dfce89791/1029_0DT-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_0DT-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/ec3a8959ee12eed7e70b84e35c7fcf/1029_I2R-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_I2R-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/e483b2fbb254c5e9a37c55b93a7403/1029_BSWE-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BSWE-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/89bf8c2cdb51f37c456f4d405623f5/1029_BK2H-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BK2H-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/641d24c4abee8b52349cc96a3126dc/1029_GW0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_GW0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/d26905cffd186a8d9cfa104705845c/1029_0NX-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_0NX-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/b32a282d4d115fcfae770e648cb2b5/1029_56D-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_56D-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/7a07e4f4c71e04bddb5313700d9a47/1029_1H5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_1H5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/43c778130226cc990e26e8a26a197c/1029_BICA-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BICA-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/2f/fd2c8c421af432b1aaea36a15a5fcd/manifest.tsv manifest.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/1425702719cb603873c2c948b0a6af/1029_05O-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_05O-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/7e099b019eaa329cc9e1a240f0577d/1029_E36-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_E36-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/e352be5d55caa9cface06602a38607/1029_GZP-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_GZP-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/6a4b0522d4b4ade1064bcfe3c1afe5/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/b3d53138ab306c2a17248775fdaec9/1029_BDOZ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BDOZ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/85b9edd1554431279f78fb27e6f14b/1029_FXQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_FXQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/55ce6d30aabe3fbe709136f6de717b/1029_I5W-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_I5W-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6809c7c068cd11c68d2f9119e456e1/1029_BGFD-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BGFD-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/4a1d317abff9e68436aa586a1dd37e/1029_8AV-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_8AV-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/a172b25cd028742dc8c47916cbe721/1029_DV0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_DV0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/3facb31a583a4c0e50126386e25381/1029_7Y1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_7Y1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/6c96f0e33884ed6997fc997bd1b2b8/1029_BBS1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BBS1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/c194e90b3d41d8e304ddfbf2325040/1029_3OH-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_3OH-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/81984806fd0196a0d33a14c385964c/1029_BCTO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BCTO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/cf9f5309fa1b88a94e9ecb303fde54/1029_BO4Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BO4Y-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/1f9e236c33273621b8f28b70ec5d34/1029_H0U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_H0U-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/7cc299a68db0c5e59ae78e1b7babfe/1029_C35-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_C35-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/b659a7ac6374375f46d4c008005e84/1029_H7F-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_H7F-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/6a4b0522d4b4ade1064bcfe3c1afe5/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/b8b1e48caa63b19bfbd4d5f8178f62/1029_BIHO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BIHO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/c4bcda736bdc4cb70ca7e0d9d194a6/1029_BQXQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BQXQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/60e67b69ee1bcd12ce7fd7c58ffa7c/1029_4J3-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_4J3-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/38869a656d7767e81a431eb64688ec/1029_BRTT-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BRTT-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/a0f547cee112be22594d63db23f371/1029_BQD7-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BQD7-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/24fd0e95c5c8e214ce417244fe19e0/1029_I8V-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_I8V-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/14797ef889aeed89d71e53ae568234/1029_G94-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_G94-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/3e9d9bfcf6807c96fcff56e8a1b10b/1029_BFKM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BFKM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/32d61e310dbc348c99533870459e76/1029_BS78-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BS78-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/7d1c8db9c441c282f1695ed5be98f4/1029_BQKE-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BQKE-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/2053fecb01255a5f150ba2cfeca64a/1029_I0S-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_I0S-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/43f11500217b86005430f94bcee8d5/1029_BBCQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BBCQ-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/53c112018733f405e531752a0afaf3/1029_8BO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_8BO-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/eaf24629598dc2e8289327330f7eed/1029_4Z2-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_4Z2-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/375d768e687f3a43d3956a998f81ea/1029_H0A-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_H0A-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/0183e39391981ed94cadc101a45acd/1029_H5S-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_H5S-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/8d5cc0ecdd6ad996a250ab06743db3/1029_BP21-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BP21-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/13c90ae9bd14825218b8a1306b6931/1029_BLU1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BLU1-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/7ebddac1ac9b912da7e81a9bd405d3/1029_BBOC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BBOC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/f6960153fbd24955992bd2c027d203/1029_BCB6-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BCB6-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/87f500172c6c02723937a65293b428/1029_FWL-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_FWL-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/57b87ac1be315ed645980a2a293abe/1029_HX6-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_HX6-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/60bb5502f7a9b420b43b55dbb563be/1029_2IN-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_2IN-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/5aff09d7fee5de4e4172b985bfcfce/1029_EFW-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_EFW-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/45847f9804ee35d84112bcd25886fd/1029_EMM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_EMM-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/da708dc9fc2bab06403baa138409d2/1029_1G0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_1G0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/355453f50d392605f22c9556e3e6db/1029_HT5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_HT5-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/7409f6e927cfe5b4f6f9b2a84378c9/1029_2LI-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_2LI-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/f736f2d02d39292a0ef04c8c65ff50/1029_BJH0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_BJH0-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/e8fed529c332b99242b815ffcba01d/1029_DOC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_DOC-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/d312e3372fa6be446ace2523b9be48/1029_H3R-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz 1029_H3R-N1-BDNA-1_235YY7LT3_1_probes.tsv.gz")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (91 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/d3/6a4b0522d4b4ade1064bcfe3c1afe5")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/6a4b0522d4b4ade1064bcfe3c1afe5 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/6a4b0522d4b4ade1064bcfe3c1afe5 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/6a4b0522d4b4ade1064bcfe3c1afe5 || 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/d3/6a4b0522d4b4ade1064bcfe3c1afe5/.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