#!/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/e5/f4f4aaebc3e8ff9732fd8c0d067706/.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/f7/9ed964c14c4a98a3cad78c5c3381e5/659_bTq-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bTq-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/9d68fb387d3e94a4aae33a5b0aeace/659_wQ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_wQ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/cb5e60cac0d8ceb00b617f50247d58/1136_42A-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_42A-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/21ac6c32d13f71617da6416b2251d5/1136_3YA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3YA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/bc5e7acf1ae73af7668067e6d1e2b4/1136_491-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_491-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/7a50c4393c6ba9009fd554cdd0e2e4/1173_CH0-N1-BDNA-01_B23KGCJLT4_1_probes.tsv.gz 1173_CH0-N1-BDNA-01_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/5a2cd55d9095fcf1f63dbb781f77d3/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/6eea56bdb52726cfa1982126bbb89d/1029_BMFL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BMFL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/bb5d3f144ac56f6611febd5d6abf19/1029_0W2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_0W2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/5a0412d69555ad17fdba50553acd20/1136_63V-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_63V-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/80b617ca16a4110329479e6d557ce2/1029_FZO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_FZO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/c743ad4ab6f530a47cb74e91ef3de1/1136_85O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_85O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/7ac3f913bcc8fc210383916f3de875/659_cVw-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cVw-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/1fa82c72025c08f4a9283be6cf1543/1029_GF2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_GF2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/9264f777bf43596f8480e05be745dc/1136_7OW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7OW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/04fe25b84bdec11b2160be3a9c3301/1029_BF84-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BF84-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/307f6dab63bc96ede7b95f9265732a/1136_1D3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_1D3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/6b1fbb4fc3df3314d5dcc81e1cdfa4/659_Mt-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_Mt-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/c45788894fb5c16f278b1e6e93661e/659_djb-N1-BDNA-2_B23KGCJLT4_1_probes.tsv.gz 659_djb-N1-BDNA-2_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/4ea84e9f045c061b7770ec93063301/1136_5AC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5AC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/e39231de7dc0e766b418d679657718/1136_32X-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_32X-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/6ea570fa53eae9b5ec8065c47ce4e5/659_1q-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_1q-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/e6bc470fd80d890c8f51ec1a961af4/1029_I9B-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_I9B-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/e25b4a8bb9e5565ba6a65195ad4879/1136_6YX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6YX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/b10338c020a156a706e85a39380bbe/659_bCu-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bCu-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/92388a82deebfb74d46f60ea00f1e2/1029_YEA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_YEA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/77032bb4639ccc2232d5c85ab6aade/659_dts-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_dts-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/3cd2b41569c0c6601eb82ee4b548d1/659_dHy-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_dHy-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/51e76aff7abc6fe84d0abd4bd1f501/659_ecd-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_ecd-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/0c34cf0de478129e8fe745da051bbc/1136_76X-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_76X-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/09e7a424ba04de8729b0ce3da14377/1047_BP-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_BP-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/0a81f81d3228937b58de3b8bf9e7a7/659_8h-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_8h-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/6a825426e14faf0fef0d6a698d6844/1029_G74-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_G74-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/665764f121c615a74956aae9864f4c/1136_5P9-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5P9-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/2f4d7ccf110094a720d83739ab1d81/1029_BLBE-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BLBE-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/baf8c33b7c82f5b3f048f183288431/1029_11H-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_11H-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/4377c2d844bc50178967f1e175a484/1136_86Y-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_86Y-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/9ec129ca07fc34603c4167ead1972a/1136_0B1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_0B1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/c7b58146fa44a72485ad8aeba0f9be/1136_253-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_253-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/685642ba3eb542fd00a46cf22dd262/659_dQk-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_dQk-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/c52c08aa3e6905ef853e2f7fc625bc/1136_5PU-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5PU-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/00486fcf01b442381972b3a40599a5/1136_50G-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_50G-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/f48d06fad4e293a66eba4afcb90ebd/1029_D5N-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_D5N-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/b93ed601407d520b9830ade713743a/1047_JG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_JG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/86f790da6fbd554acdc6a673b0e68c/1136_6NT-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6NT-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/9bd3027ae7aba3317a3793d3d12dc9/1136_06R-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_06R-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/9bc9f38d67bf205a5968217a460368/1029_BGBW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BGBW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0484664df151fbd6f6ef06a2b46df7/1136_4EF-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4EF-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/f88bb019bb0db845367ec94c898e8d/1136_81F-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_81F-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/f4b154efc2c51427e88ed8a1c6a8a1/1173_JXL-N1-BDNA-01_B23KGCJLT4_1_probes.tsv.gz 1173_JXL-N1-BDNA-01_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/356bb14c8233aad376badcf6ede244/659_cRB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cRB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/15dcbd4aa5bc5bfa534550b6e77af3/1136_3S1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3S1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/51e0a4d0c8a80136fa52305d16fad1/1136_5L2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5L2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/79624bc3888f6a593b3e562f265429/1136_8DV-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_8DV-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/708623fe06a7d7f68b83df68e0525a/1136_56P-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_56P-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/8bf7c05e3a75e756624bc2e27a8194/1029_1CU-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_1CU-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/5f2c850c23f22a59ea1a7f8fab8d64/659_e0S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_e0S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/4133a2a4677aafe6acb5799a7344e1/1136_4PJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4PJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/f4f4aaebc3e8ff9732fd8c0d067706/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/bc75964814d0af189ecb11823fe700/1136_4VB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4VB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/0e3e885c434de40cb542f44e16cacb/1136_4GR-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4GR-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/d066d52daa0a43caaa2b68d8cf03bd/1136_7PW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7PW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/8cdfc93aa77c203a9e55cbefd2db78/1136_7Y8-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7Y8-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/a1fe3860427226b92dc26d0e44e1ed/1136_5Q-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5Q-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/f4a49d42185c0ad53199854090cb9c/1136_6G2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6G2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/a659f7010273798ce3929d48362576/1136_6BL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6BL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/5e6ea40bf2b68c2296af722da2c965/1136_6K2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6K2-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/05b0d2e345479f889a3a3af0479249/1136_46O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_46O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/a05ccab7246e13cbc906ec01f1d748/1136_4ZB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4ZB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/5674ec21fe79a7487a6ac615eac192/659_cuO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cuO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/3e2fd23f3e4f93ba879fb331f0325e/1136_5OE-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5OE-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/5d82ef2380942b9161bd4fe6b9a5d7/1136_6D4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6D4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/b06934756b16df1c0e42f55cf637db/1136_654-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_654-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/3f7e4910f2e5c42a1911ea555a21b6/1136_4TI-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4TI-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/3cd7f5beee8a0f9736fe8428ac9c3b/1136_6DX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6DX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/df1ebc8497b20dfa6d9ccb1229491f/1136_7GC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7GC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/ea4f28cc296bd9b038c2cac2dd4065/659_cfy-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cfy-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/38df940467cba00a536dd1212a122b/1136_7QM-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7QM-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/c8b5918fafdca09c70ec92d43092c5/1029_BCAN-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BCAN-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/b8b57cccf7104d714bf4774ee2cde6/1136_5KC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5KC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/e555f0adc7c9a811f8ef89f96251cd/1136_6EI-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6EI-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/076410126d616cf573dc20c7cf9808/1029_BCAP-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BCAP-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/b5498593d92856567ee0fec6a994b6/659_Kh-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_Kh-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/ee216b1b680717e04895c557716d68/1136_5QM-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5QM-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/a8cbb35fb21b12bfafba74e6cf69a0/1136_283-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_283-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/a288a79a7e12601b178c78a8f8e7d2/659_R1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_R1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/b559c4ee449507eab4bd7877dce94b/1029_HTI-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_HTI-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/6f91c529f218b34ddb8b69d72de6f1/659_d01-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_d01-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/0f2699e1a2c3f4fa2a30da3d6e9361/1136_2LG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_2LG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/f8ec61ff0ca752eef52ef96a3883ba/1047_CO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_CO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/1569a85367bd8c7e65e8720fe9f406/659_bhK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bhK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/baa313a0844db681c025755c8eebb8/659_eKx-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_eKx-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/8ce950687a45985de39d752df22bd1/1029_IUJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_IUJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/66c2fafdfc03dce16b0f2f0c273572/1136_5QA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5QA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/8852433925ddc4d34c515ef2cdc20b/1029_I7E-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_I7E-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/f5701c7293ce29281fd7bcf2b77e62/659_bjq-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bjq-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/b8e68ff572f01c2a2c5e7aaae593be/659_bUW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bUW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/8fbcf55b164251ebbe716d365434b1/659_cRa-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cRa-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/e38303340fc22b0741f58c6b571af9/1029_N5D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_N5D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/669a087b59ace1feb3fc4e1bd552e6/1029_HOD-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_HOD-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/4558b557e92005fe85fa7999174113/1136_3D3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3D3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/5711fc47895d2c1a57256235218d0e/1136_87O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_87O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/f5a90f449b95308df3b64789f28ff8/659_eZ4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_eZ4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/909030c5ee77a80f7b50cebc2969b1/1136_5TB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5TB-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/7b0838b6bc3972342adf5e7cee690a/659_dm4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_dm4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/e1ed5a69e5a3141478836dcfcb4fad/1136_4DO-N2-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4DO-N2-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/3d53668919033df44928734419834e/1047_GD-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_GD-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/76374baa8a851d630b56d805f9aa76/659_rd-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_rd-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/157fcfa723de37fdb1c34f22d1bcb4/1136_5ZG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5ZG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/ae24ad2424085059e52b323f5cd4ad/1136_7JV-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7JV-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/d0cbf172260f6fd8165461788e4d16/1136_4Z5-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4Z5-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/a2bb5e73c2c7084218a61340481812/1029_FVW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_FVW-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/20b295965ac9daeebe3137445e2643/1136_8B-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_8B-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/e067f35574c1f0a5849e12c69ee7d4/1047_CJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_CJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/f163210d5641d5f16656f560c14196/1136_3O4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3O4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/b998ed2cf3b63749b2262e9b1a6989/1029_FRC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_FRC-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/8cc12ac0371ace7a9355c5e4f3ee02/1029_FZX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_FZX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/cb039f0333e79126e7491a60724429/1029_0I-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_0I-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/f18d92dbcf0238423350acd8e4c2e8/1047_BE-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_BE-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/eefe1842f43071793e7ebcad35540b/1136_5V3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5V3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/4809bc53f5d4746658d0a8709f29bf/1136_00H-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_00H-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/7697cfc0f560e68023390f5ab48a32/1136_1WZ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_1WZ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/23da69f329452098ad9bc83ed3b32e/1136_1X-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_1X-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/628b1ba037d9ba0cd78aba3e1f242d/1136_85T-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_85T-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/868e37b12a7e48a6f4f051d0f53a17/1136_49M-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_49M-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/d403a7dcc6351cd583ab548fcdc965/659_bgw-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bgw-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/d477f4c2d4f3a1898db7c95b3315d7/1136_3U6-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3U6-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/6ab821fcbab9a2dccb9569945e7ef3/659_Fr-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_Fr-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/1a8ae22bcd93f916b926ee140c6406/1136_3LU-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3LU-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/a2bc19424585224feb513064003673/1029_BICJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/6c53bf534bee71174fc917cb043881/1047_5-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_5-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/a7f6c389f878a9f0bf7d00fa735917/1136_1EO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_1EO-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/1f/e953bf0981839ef14442cd93a52ad4/manifest.tsv manifest.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/aa7fe7cd5d7cf26c05d5441698cb57/1136_6TL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6TL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/47b51183916386f44b5fa161845dd5/1136_6PL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6PL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/211d0e126fe2bbe9a05bacd0607397/1136_67D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_67D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/f4f4aaebc3e8ff9732fd8c0d067706/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/631f604a8448943416552d68eeb2d5/1136_5JK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5JK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/b768d63cd3e8f539b9b8d3b49604a6/1136_45D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_45D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/20e6dcb0d1a5af62c2d3f2d84d7246/1136_4C4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4C4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/501a1cc1242430e3643e1769705503/659_bQZ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bQZ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/b4d9bbb873a71ae112eeabd510d3f1/1029_16G-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_16G-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/7da27bd27d0a983440aebdf44c3701/1136_1EQ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_1EQ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/50b1f120af25cfff1c766d569fdb30/1136_3MV-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3MV-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/cefe4bbcff84477e2809f417dfa847/1136_4S7-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4S7-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/b6686c81e65b78ef89505fdea4109a/1136_8F1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_8F1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/a33e1a9d5ce326e70cd302ac8a7620/659_d0M-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_d0M-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/95c7dd014907613d3989ef3b4863f0/1136_85P-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_85P-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/9831af27cd732e93cf52734130220d/659_epG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_epG-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/510f56679a2992cab4eaf4087a625e/1136_77V-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_77V-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/dbccdb75b6865cbf499e26d22ab5dd/659_cAa-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cAa-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/2968bde31a0b9f873062eb5cc9cc1f/1029_T05-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_T05-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/e0f262157e8a427a2fa13efff9086b/1136_27F-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_27F-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/3d456e071a1b9d55ced4489f6ee9b4/1136_65P-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_65P-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/f77b323b848051de8c9d9b149e9ef6/1029_BH4B-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BH4B-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/8aefa39d7ccf3a67d420dda95d17e5/1136_3WJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3WJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/374d943b8f90c575401e25ca742ca9/1136_55O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_55O-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/6234c37bd104f627bc83d1ea038b8b/1029_1XX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_1XX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/5b651f16c6e7b851e78ce8efa2bf49/659_bR4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_bR4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/787b06e79b0b99ca3bc8b74236dbfa/1029_01S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_01S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/50c3c31b3309d47886dde768f8e121/1136_81M-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_81M-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/7cf70cefc3ced62e8107b3eb2eef76/1136_4VJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4VJ-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/800af42e1579169e50ef3c933d5335/1136_3Y1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_3Y1-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/6c71c790e35546a850b041e68bab2d/659_egp-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_egp-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/300ef6953b8f68aa110235a5e30bc3/1029_BAE3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_BAE3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/2c7fa9082fb827762d49fdbe4d71ac/1136_4D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4D-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/c234f1282ac017d3f3f8a9b4c594bf/659_buj-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_buj-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/aed976a1aca0f00dbb8504cd5f65d2/659_Lx-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_Lx-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/c4af61298e30defca2e486ddfd8e35/659_cAd-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_cAd-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/049699812554116f0d7972cbe3ae0d/1136_6J4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_6J4-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/42d2b431240d236af03c5c6cdd1b82/1136_7NX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_7NX-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/1ea6fe26e962dcc1c675a585614793/1136_86S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_86S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/c7c1149f9b6bc941512748ef621b9d/1136_81N-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_81N-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/8ddaca505056c8799800c6d3586d33/1029_IKL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_IKL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/6b23874dc52c9af9ee09838479e44a/1029_IWL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_IWL-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/b459ca8c765f3a9616120d9f76cc45/1173_QJL-N1-BDNA-01_B23KGCJLT4_1_probes.tsv.gz 1173_QJL-N1-BDNA-01_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/aa949085b96a07b960e85ea87feb20/1136_5U3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_5U3-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/1f8bc4617c2e7c023177e501999cd4/1047_FA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1047_FA-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/c1ec8e9bba3801a228c1f1d9aa3c9f/1029_1BK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_1BK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/09ab65fd25bed39a2aa2c53d6c6c8b/1029_F0L-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_F0L-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/83b9285b9808fada648dd028dd0641/659_mK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 659_mK-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/d2640a9abe673866e629f3210513f6/1136_4ET-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4ET-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/060c79e126af7b32764df11fe46f54/1136_4XR-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1136_4XR-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/6e9af9f11339f5905ff3611539f5c9/1029_IYD-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz 1029_IYD-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (184 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/e5/f4f4aaebc3e8ff9732fd8c0d067706")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/f4f4aaebc3e8ff9732fd8c0d067706 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/f4f4aaebc3e8ff9732fd8c0d067706 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/f4f4aaebc3e8ff9732fd8c0d067706 || 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/e5/f4f4aaebc3e8ff9732fd8c0d067706/.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