#!/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/4e/b9612ce73e6ae99b1d099298743176/.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)
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/15bd5f841830fdc9f8debb952cf8f8/1136_2FB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2FB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/4dee2d4e6082025d52e12332bbb222/1136_2RB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2RB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/90316ee50cdb58167cd6221a77f7bd/1029_BRU2-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BRU2-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/a2afa3e67025033ff4df6c674e11fe/1029_2ZR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_2ZR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/41e25b2fd8c5f70a39e5483619399f/1029_MKP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_MKP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/176076e9fefe91c58eb86a2bfeef74/1136_2PG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2PG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/37f4d6fc1f25d5e239bcfad41c9a76/1136_2X3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2X3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/32f34cb9a586871bcf37b492f32b96/1029_LGO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_LGO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/762bddbc427c236a8d113a146df113/1029_D1G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_D1G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/5239ac876e4a45e4c779f8858ef99d/1029_BAMB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BAMB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/00d175b27b941d654e07817236ed69/1136_34R-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_34R-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/ff2f447becfaf0427eb24aa55484bc/1136_3EG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3EG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/aea35a2aa7a02d7207e41b3769f3c6/1029_3SA-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_3SA-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/1ddb9d3bac028603eb2a9e0bc34a89/1029_3OA-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_3OA-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/6664200ce090be6a389f07941aa1ed/1029_BDHI-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BDHI-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/fe561ce018eec6ec02ded9fb3f87a0/1136_2SK-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2SK-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/ddb609eed95b0c138f8b31660e7358/1136_17X-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_17X-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/0a9facddbbcaf7b179dce79135a317/1136_2TX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2TX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/97830cf4897bc0151e26a9355c0a12/1029_BHJD-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BHJD-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/253160f989c35c67ec3cbb7487b588/1136_3RW-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3RW-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/7e975876f15ebc0ea0040d059fdab3/1136_1ME-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1ME-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/4e0f77c6f476d0987810168eef4a02/1136_37O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_37O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/aca95aaeb46490f61e471cf834ee89/1136_3DY-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3DY-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b52c94bc45fdc6b57f4004230d6d6d/1136_0HE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0HE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/cf7c63a7c0ed19c4ae171d291d240c/1136_08E-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_08E-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/b5ea34978b24a23d2b5bcb62c9f40a/1029_HGR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_HGR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/345765ad77aef525cfac4bd55869be/1029_5KP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_5KP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/122a08f536db19faf737ab3503be5b/1029_MHV-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_MHV-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/53d3582a79d0aa74d97ff8607dc78b/1136_19S-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_19S-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/d9fe7b452160ed05754e8d6d4c080d/1136_33P-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_33P-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/44b13bc24abbd22569e6f7edeb538a/1029_U0A-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_U0A-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/0418a802bfad8591f68afe46c581be/1136_1HP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1HP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0e1b5c4b514dd98612700ff7464ba2/1136_0R6-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0R6-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/967639093022ba98b7524faf1f6d76/1029_BTBG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BTBG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/84d95b535c57310dfe8e4e870e376a/1136_1Z7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1Z7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/e07b8cd865bda8eacd98fdeab76c7f/1136_002-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_002-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/a51872b4aa8360c1ee41f08798438a/1136_2OL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2OL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/c46fdaf26e579395751fdc784e74d9/1136_1H5-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1H5-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/72360d340c02495ab37c29cbe7a89d/1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/65a500ff6a8888b5d916cad80ab335/1136_3DG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3DG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/fd9159b9e840b6563c1f5b0b2742b9/1136_36B-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_36B-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/8843b6b9a3b08c0528b8a0c78e69e6/1136_3DL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3DL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/9907747f943dfff8870c12f497ae42/1029_VB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_VB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/504766b8ff4e9ceda93014c855584e/1029_EBU-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_EBU-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/b7403aadd2eb0c2e5989f832f63171/1029_2RG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_2RG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/4ef399192e57630c51aace4bd743f5/1136_2IL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2IL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/7bf061804ee6d34d210678f3fb2207/1029_E5O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_E5O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/0f9f6ff81d9d06942a0bce00c29ba5/1136_1RX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1RX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/cbe904fa1cfd5b97cf04d4c56c577c/1136_0NF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0NF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/0a718a9b621dc42dc25c346f954571/1136_2ZF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2ZF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/b9612ce73e6ae99b1d099298743176/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/588ab18bf6cae7a7b750c68e3ecfa2/1136_0QS-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0QS-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/c98b8de490f9fc4ab2892fd022164a/1029_TA7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_TA7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/921b297e31e111addce0e768686cf7/1029_4EU-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_4EU-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/0e3df28b25dbd36d277effb5ad0e3c/1136_303-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_303-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/47fe63d64b94781b40ccc204c9c205/1136_0G3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0G3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/bf23f00f33368a3747fa0c092b27ac/1136_2V0-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2V0-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/e04f56a09f9154119641c5dd8e5222/1136_1NE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1NE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/18911ad31f9de0fcb029914bf27f5e/1136_32O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_32O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/d91751a2cd6a136f8595646f608859/1136_2KZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2KZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/aa0b31a429d01b7febf229c6876327/1029_BDV5-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BDV5-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/702a609c6952f91227c8ac5c11c288/1136_4R0-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_4R0-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/2116f1ebb1622670b8aff4703e6105/1136_4QO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_4QO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/7a90965e8eeea20e3c58095cdfcf35/1029_BSNE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BSNE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/6ff9a8e91c83bea0afbae1ffef088f/1029_BMYS-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BMYS-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/9a892f750013eefdf2111edbf7996c/1136_2GX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2GX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/6d506d4ef577eb9d0e14c6ee3f27df/1136_3LK-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3LK-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/fcc69dd370e8bc738ed405ac751ae5/1136_2NU-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2NU-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/2df7d350381d889bbd6da5326db014/1173_LV7-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz 1173_LV7-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/843b5fbcfadb4a4eb63f21d6148504/1136_2IP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2IP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/4263b1c8f5bda0c6931e1b2f9d2841/1029_JOY-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_JOY-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/4b6cae36e58d61abfdadf832520b23/1136_2J1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2J1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/5a2c45c7fbe5ea1226a9c840e09eee/1136_20Z-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_20Z-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/25e4906421e568519d5d961be70a0d/1029_1I1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_1I1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/ee24f44c16480c0bb34a265f4d6143/1136_2SZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2SZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/84bd05ca8ba27fcd992fe73bc5cc50/1136_2UQ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2UQ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/f8687a44b5520ea142befd6f8a598e/1136_0YR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0YR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/ff669ea90ed97dd0e54d0f27589861/1029_GEO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_GEO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/65dcdb7c1ef2d12195ad9acd61e10a/1136_2VD-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2VD-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/55bb7c92dffe25e68df40f9de8b81e/1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/2662c483330322a31f8750f3d2a025/1136_7AL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_7AL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/79f334934c8f69e9b815708e54e772/1173_Q7O-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz 1173_Q7O-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/83ecd6c3f8e9fb843a50549ca0e59a/1136_1N2-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1N2-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/2818088a6ff9653b8b980fa3d71e27/1029_D5L-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_D5L-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/7b35162c08aabcc7f6ffa2e2209cf4/1029_NOY-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_NOY-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/e82acf2eddf8bcf9e27495791b89d2/1029_SH1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_SH1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/9b2b76218473ff0eeb0f6af33ef390/1029_N4U-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_N4U-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/82a8572ee69db5eecec5e06684431e/1136_7K3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_7K3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/f404f7c7717f3516ff2bc09976c0e6/1029_BA1G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BA1G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/af63175c9e668a90178de212c1f3ea/1136_2X8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2X8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/7bccdad425ae7393775a00f58b8349/1136_36K-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_36K-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/ad07027092412bccff20873e6ea6ec/1136_1ZF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1ZF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/e443042a6aa33e5f04b10c46b2baa9/1136_22-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_22-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/4015f60f3e966f39f7bfc68dbd3e33/1136_391-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_391-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/49d3389637fe3649d3d9941622a9aa/1136_019-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_019-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/10930eaa82ec8a8caa966045ee2f1b/1136_30F-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_30F-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/7874ce9d5665147924dae50a682c78/1029_Z0K-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_Z0K-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/611c1860bdf22db425e9caf7400f7a/1136_0YC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0YC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/62fa4aa9bc322ecd1589b7f23eb60d/1136_281-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_281-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/380753e4391d0ac2f9b7fbaecda018/1136_2ZX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2ZX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/3e4d1a527df0eadf556fb838021d39/1136_2I7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2I7-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/204302f0650182c83a82069210b875/1029_BBUO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BBUO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/242375fe9e1ac975d3296e5dc0ede6/1029_BPB8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BPB8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/9e34e1b55aa9fa12b772e0e64bf586/1136_2RJ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2RJ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/bf16730fc22cf11b0932d07578450e/1029_QEF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_QEF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/cf7379812e3963e005c092cfa64c4b/1029_BN1U-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BN1U-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/0c01e42fe6ddf1e3df9bd8e912d3a2/1136_43A-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_43A-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/3e5a31267857712ba4d6a29e992c47/1136_08G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_08G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/9fd134b192063e468500d83b3fa5e0/1136_1E0-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1E0-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/65753840041bcfc6362b4b97243371/1136_1DO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1DO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/1e3d3046bc45ff1c34709e635c79ad/1136_2LO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2LO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/a091efabbfc8c61fbc46bca3e1807f/1136_1ZT-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1ZT-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/325921d15cc0b9f51ace51d9ff66d9/1136_355-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_355-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/d4c315da034e8bd0492a594cbba8ab/1136_3BO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3BO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/2823499cd2d2b4b9876709bf1ea5c9/1136_1RI-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1RI-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/8f59960739011a6142b03342e63bb5/1136_31I-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_31I-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/e6a4cdf1d096180e3174bef5384658/1136_36E-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_36E-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/64466ad83ce64447855967c7d2d067/1136_0ZS-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0ZS-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/573e639eb3051e93af51c57964bb12/1136_1AK-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1AK-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/702f09ab9a372aa1a32c37353881fc/1173_RQT-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz 1173_RQT-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/94eb4c82aef26ac633d38ae6dd5cd0/1136_12C-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_12C-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/35df60a110666ebb94e3a661fa2383/1136_201-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_201-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/f2/1611af2c6c90752d6302b4f9f8bd2e/manifest.tsv manifest.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/70ca65b222348a188b0a6af0e3a82d/1136_1J-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1J-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/7262cbc0f993b6b48c0ebeee60ed79/1136_257-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_257-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/a6c1a4666e4992591d500a92e61248/1136_2W2-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2W2-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/e0530269543304a253f3bc0ba4e53e/1136_382-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_382-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/76ef0a78cdfd05790811c8f0965d37/1029_X7W-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_X7W-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/b9612ce73e6ae99b1d099298743176/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/3062bd6cd1b3bb1381324cbb40bc9e/1029_BM04-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BM04-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/efe8f72303aef2e8886e7a2e796ef9/1029_O1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_O1-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/eb59a2c4132852be758abdf0317ef4/1136_1OL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1OL-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/3dc3207adbe89ed82f6fa14f0bba06/1136_0ET-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0ET-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/2fef20f5f6f9b94cd848fb029d61c4/1136_23Q-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_23Q-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/c7aa5773f50d3afb5605cf92742366/1136_2SB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2SB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/0bb98f6609987da02e9d6e063d0e8e/1136_30B-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_30B-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/5807ecb3602d29a5d91e297c3173b0/1136_3FG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3FG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/67866bbe3c6991b1ec370d4ecb9620/1029_5CB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_5CB-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/34c0a67fe112d39f534d9fff763c4b/1136_32G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_32G-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/6fed115da59b27739f2dd7b2e593db/1029_BI1W-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BI1W-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/8b98040d8424f5807d7e1022842861/1136_2U8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2U8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/1dd30e938f8b4889580d59ec85ae1e/1029_2PG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_2PG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/f6dcc9072b5ef6795240f5f77b8d00/1029_M7J-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_M7J-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/d08a2ead38ccea16c9cfb0c2c04381/1029_D92-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_D92-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/462b9c2829b33784cd0f4cb15fd3ca/1136_192-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_192-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/e43e3ef5155d1eb7c72bda2f1dc49a/1136_6Q8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_6Q8-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/6ba8c4fd9a49d9c1c75486ee3fb4a2/1136_3CM-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3CM-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/efcf3359057ecbdc65da7ab9a46fc6/1136_27L-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_27L-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/8e9619056d6692dad5435913c438d2/1136_0TC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0TC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/894da9e7cbf1d24f9bd243b3208404/1029_BMKP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BMKP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/41a7cb2c5e84f234beb0e4bf997b91/1136_2UX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2UX-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/2535c54719e4f399715cad02941175/1136_0N9-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0N9-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/97a72f2db17541a3cf3400024f96f7/1136_1QF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1QF-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/e6f75821731249e4897b83ba1b18e9/1029_BGGP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BGGP-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/0c4c5fba5887436197bf5d70a27bc3/1029_BB2O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BB2O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/846d8a0ad0b3b044e91f0c5d5b16ec/1029_80V-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_80V-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/cc7ad30add934f58e5decc608af2d2/1029_HLV-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_HLV-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/29574bf90debe9dc44f5bdcbd9e064/1136_31A-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_31A-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/d3273293a68b1d8bd4871265e9c65b/1029_BOLT-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BOLT-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/505e568d8ebbbc12ef1629d4a5741e/1029_CE3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_CE3-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/86d9b94fd78e3bf119fb07ebbb29f7/1136_2I5-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2I5-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/41834799a6528dd241f78fef3fbe02/1029_PLR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_PLR-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/cbf577ffbbf11786a5f81a58f9a9e0/1029_BAHZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BAHZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/561587db2e2459df9a06a38424239e/1136_2OO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2OO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/d247b8c1ce1608e409e721a0f3b1e6/1029_BKQJ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BKQJ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/dc25c56eee7e51ec910c3279ec57eb/1136_4KO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_4KO-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/3f57e55da8c27d3988a3e5063e7667/1029_BA2K-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BA2K-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/51b3efaeedfa61b0db9ec49f6fe6f4/1136_1MZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_1MZ-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/d6dc5cd153eb2dedc7645ff8ce03ed/1136_0TE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_0TE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/c11819ac0b2be9a81f143c79ad1b6d/1136_01E-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_01E-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/8c74e88cca774a640a3966055c7904/1136_74O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_74O-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/0b993da0f6fcace85251d0db94082f/1136_18S-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_18S-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/815e9898dc8ad1d1d10af7da295e55/1136_5XC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_5XC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/905f33dded4219ae8dd586992733da/1173_KQG-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz 1173_KQG-N1-BDNA-01_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/087e90c71a7f4c6b347d2ba6aa4cca/1136_02I-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_02I-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/0372382fd717e09b2a2938f95e9f4e/1029_BJNN-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BJNN-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/6b641258b78c1a9ec1290f39844e78/1029_BIG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1029_BIG-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/2aa6ba00902de72be796dcb831930c/1136_01U-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_01U-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/7bd782de08f2e72b3468757c547a31/1136_16Z-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_16Z-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/27ce4923573e647008e982dd85be0b/1136_3AE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3AE-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/c1d8c86aa65b7ae1ffbec323cc82cc/1136_3F-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3F-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/d82913826ee3cf6f807fc06c1b8884/1136_2QH-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2QH-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/bf2ba104a3922f47650975b64f0e2f/1136_2PC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2PC-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/7529a7145330d7ed65a3f784f755f6/1136_3AW-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_3AW-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/40045a3f1eba3a58c251536bbf92c0/1136_2S-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz 1136_2S-N1-BDNA-1_A23KFG7LT4_1_probes.tsv.gz")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (185 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/4e/b9612ce73e6ae99b1d099298743176")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/b9612ce73e6ae99b1d099298743176 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/b9612ce73e6ae99b1d099298743176 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/b9612ce73e6ae99b1d099298743176 || 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/4e/b9612ce73e6ae99b1d099298743176/.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