#!/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/84/843a1b434e4df28bc36574452cd345/.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/b3/63437a024790fdaed6137f660e6e3d/1136_4DC-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_4DC-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/6ab6474ecbf514e1911ce9ff7026a3/1136_5SH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5SH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/ff670854e98c4b4b3ab9f1ba2f56c0/659_dYT-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_dYT-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/2ba814e63e0565498962e8ac0151ea/1029_4FN-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_4FN-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/1f47635634a26a56f01ae7e14deb16/1047_I0-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_I0-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/3eb4b4a7ff7ded76ed39abdc85cfbe/1136_4JH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_4JH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/36aea5655d1eb963279aa911741204/1029_S8A-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_S8A-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/7aca6983a88c66eb1ec9106ac859fb/1047_IN-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_IN-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/5dc1a64a96bfbc4ad421c390f00bc2/1029_7ZM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_7ZM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/a77dee0c0d9e4a27a394609e99f590/1047_IU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_IU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/8bcca7b4c32945592196ab486ade26/1029_HSC-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_HSC-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/11f0d88fc4c3d95a2f762298277e1d/659_drZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_drZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/6d4b5f550a4e424d8d6b4e459849e0/1029_GB9-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_GB9-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/83bf64d88c80fa3adea29cb0082ab6/1047_GF-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_GF-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/4f924fd8cb1ea2748b6ea215dd72b7/1029_BTN7-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BTN7-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/95fc2824c3de4b943ed365762a97ab/1029_IBR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IBR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/275b78395d7d7bac753f01a78a5121/1029_HWM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_HWM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/0241291dcbdb45b6505ff67830227b/659_ddv-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_ddv-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/bed11a0717f6b555e2ed3ccfd2ae3a/1029_G9D-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_G9D-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/c709538af808d988a28c9120cc5cae/1047_BJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_BJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/e6b3430c178268fa184dbbf05cf315/1029_WFP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_WFP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/76217b68631b2d0cdb7cfd2ad73e22/1029_2VZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_2VZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/4e3742e949da89fb7711e217148afb/1029_36F-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_36F-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/d8af42b15abc11dd49f7ec1c226a9b/1136_3YU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_3YU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/b025fb25978cb7e2dd0e1ff9f4e9a3/1029_LJN-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_LJN-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/d70daf29c19dec8e2674269589dce1/1029_NQS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_NQS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/9773415367c5b340a42d6f0355f759/1047_CB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_CB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/65395f0f71622acd9341ab59134a49/1047_E3-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_E3-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/7e3bad7e6b8bb92060eefa303b96d0/1029_CLD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_CLD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/97182212ac23cc99bf34b5e86e5103/1136_0GQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_0GQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/39da6a4789a5e95566e5f691dd296d/1029_BHOU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BHOU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/b6fe9e99fdac09a065b3932e3b6ddc/1029_W8X-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_W8X-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/998aa9d564c6c3f1fbb2ea7494ec65/659_bZH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_bZH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/a4a13ba0b3fb5760e7163999b33c13/1029_IRX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IRX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/9a931d71afb0e632b09a8b00866aa3/1029_XZ9-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_XZ9-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/14a6740944251bdd041136f3e85f4d/1136_36J-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_36J-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/b26ad583f45892494c06628e50c26b/1136_894-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_894-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/6b56aad7b09509b7e050020184d574/1047_CM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_CM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/8926e220e324cb53d3a7c233451dac/1136_5EQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5EQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/9782b837e3a7ee776bb1d0ab0ba192/1029_H3F-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_H3F-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/70735169520f8a22bc58568bb4fb53/1029_I4J-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_I4J-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/8765b20725bd5545bcfca497d96284/1136_3QA-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_3QA-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/42679baa28b6bc4b25dd9317c5148e/1029_LHL-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_LHL-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/d65863054670cf72879dab5dad8b63/1029_HXO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_HXO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/2b9d207469637a1b74b1a31ac274e7/1029_VMF-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_VMF-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/aef271fca1730548d56e60f8d06d5a/1173_IT6-N1-BDNA-01_B23L5TMLT4_1_probes.tsv.gz 1173_IT6-N1-BDNA-01_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/0f32db4c1d25c20033cd6937db5995/1029_BC1I-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BC1I-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/286849fa3024679812c2bef43157fb/659_drc-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_drc-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/29af36b01a6ec375e200875224354c/1136_4UH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_4UH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/fc0c0e1573a1a7c511064d7665f362/1047_BD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_BD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/b33af0bf3805e278738f8a414a1bad/1047_JD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_JD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/f5bd9434fb225f8f436cc3c4b5ffc7/1136_5R4-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5R4-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/2d8a6d3ec15c70c5c7294f187bfae9/1029_JYB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_JYB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/a1a48ee278f6b7368efafc3a92ab1f/1029_BZM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BZM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/0e8f4c440b03970abe8f7a365fe118/1047_GJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_GJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/1c249e5054915f27cf40cf1321b220/1047_DI-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_DI-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/51b868760933d9bf61838311819080/1029_I3K-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_I3K-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/9d9a1c15407d423fda5fca7dc68af5/1029_IDB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IDB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/a997fda5312197fd1e4dcb4aa4a12c/1029_BOQV-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BOQV-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/d54595758ea4aa4ca35d63c57941cc/1047_IC-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_IC-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/843a1b434e4df28bc36574452cd345/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/4977a20acf3aa2f46e1d92e5a05fe1/1029_BTAF-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BTAF-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/cbb66aeca366ba55474104a007b924/1047_C9-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_C9-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/3ed15b2ef3a3e19918241107d16675/659_eEE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_eEE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/3906afa8c00c19313abed1428ace89/1136_5YV-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5YV-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/1df4062e5f62f69e617603d34d7e1d/1029_WZJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_WZJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/3cbbfbc861d836655f43e4b7ca2883/1136_709-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_709-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/df28f039abaf5d3aa46f3fa733644f/1029_KFJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_KFJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/40b2eaf8666e1fae82c51a29ed712a/1029_IQ5-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IQ5-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/1d09b07b6cab00759401eebfc1dd1b/1136_6SP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_6SP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/eea73fdc2c505bdaa35eea481f89d5/1136_7VY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_7VY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/32d059ab0dd571a4ad918a03ee1a43/1029_PME-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_PME-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/41b520ae05219835d7444743376682/1047_J5-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_J5-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/098f1f77d6e94b031b2b4e73a91045/1047_HK-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_HK-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/cc25cab8ee1539d6fbdc35bb8fa179/1029_ZTM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_ZTM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/cd9f9f9760370de7d0c532144f3887/1136_6NZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_6NZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/f82b6cebe1c9ba4bfe4f311c632709/1136_5LP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5LP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/1330d385b34153f5a55637e7938ea4/1047_C8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_C8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fc82edf075852bf2e8f11daad269b3/1029_QNH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_QNH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/ed4d4ec491e8d4e0ac467cfda72e46/1029_RNH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_RNH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/e6e03a0c966315331451639102e819/1029_BS9T-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BS9T-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/6479d2b17561bfa38227313e3727f0/659_cwR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_cwR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/4c62d2489ccb8355e545daa2cf2208/1029_BS4O-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BS4O-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/c030a89644c9618de58a3e18e31f1d/1136_5YE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5YE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/bc2a45eb5778709c99fd5c962b69c8/1029_BOYY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BOYY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/70a1c7a05b4291ed0c6e20df1d5af1/1029_98Q-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_98Q-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/8e55915d7497b9c4b6141d9a3bbb9b/1136_5BZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5BZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/37baa8b28ee7b2c74e5111999865ad/1029_MKM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_MKM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/586732909310c5a77ff86819766da8/1047_C6-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_C6-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/49fdb09d87439ae1460b8d5b870854/1029_BLGO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BLGO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/9d82c54667b17f1ba12277973740ee/659_dOM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_dOM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/3047317ff15e1b33c83994caa8a1cb/1029_IGM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IGM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/eda268a483f1c904d4b9330274dc98/1136_6XS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_6XS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/7f56de4f5d3cb4c67f99bfd028aef4/1047_HM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_HM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/f8b2807ee63b285ab2e2d6a6e9b154/659_biI-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_biI-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/4d5c720e300340aa0df5a03a0ec651/1136_3KM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_3KM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/af906ff1893e22bcae63a918bcd2f4/659_cTS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_cTS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/2479bab2e5106778be302c29f5c257/1136_61R-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_61R-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/2b466216f6a8aa5a0c57f5c1ca9482/1029_BHQX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BHQX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/4be46436cb52dc55476b6fbdfe7966/1029_BSVB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BSVB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/0f6c4846c014bc12de0d569ff680aa/1029_BHXH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BHXH-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/cbe1e4b396e9c6f32b5308c9747060/1136_6B4-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_6B4-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/cdd98c1f198e38cb66f6484a4181c1/659_dEm-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_dEm-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/1592433417e4cadf38a808df83ac30/1047_FE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_FE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/56243b853c0cba3b8d5e976fbad9ce/1136_5VX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5VX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/08786404215ad2a9a17f25686402a7/1029_IO8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IO8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/c2b0c2cbef66962c04b3438be219c6/1173_NFO-N2-BDNA-01_B23L5TMLT4_1_probes.tsv.gz 1173_NFO-N2-BDNA-01_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/842c14be225342e18b86d0970aece9/1136_8CL-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_8CL-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/60ddc3ad8dde762c8559ea525015cb/1173_GXL-N1-BDNA-01_B23L5TMLT4_1_probes.tsv.gz 1173_GXL-N1-BDNA-01_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/3ed68ed423eace9277338fa4600e96/1047_IS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_IS-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/f67e654228d82f9b6735e820c4f315/659_ejY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_ejY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/58495a9800d2a63889b72b62547dd7/1136_78Q-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_78Q-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/6a63c0376b5fc29404c6c35cb91ec0/1047_F1-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_F1-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/7a7525a4cfce3609c3b2ed954b58d4/659_pO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_pO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/7311e648cdb5916f89141742359afd/1029_BG65-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BG65-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/e3cf972d98451dd6717a478d2e0ae0/1029_L2B-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_L2B-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/a88787acf421775bb078286bb1cddb/1029_SGQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_SGQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/7bbf0b39c720290d313c942857c044/1136_5OZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5OZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/9330db9fbcbd0c504b76bfd6317b7c/1029_VYX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_VYX-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/14d90ad6d50b4f191e2f34cf54f713/1136_5QK-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_5QK-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/77dd72e0c3dbc8ff5f3dec959c6ff3/1173_HOB-N1-BDNA-01_B23L5TMLT4_1_probes.tsv.gz 1173_HOB-N1-BDNA-01_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/dfcfa11c568f24d60a684595b12637/659_er7-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_er7-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/aafbb0ae6f85097c1665c6575e91ef/1047_C3-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_C3-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/5082efe8127f308df243b54ca4b9f0/1029_GJE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_GJE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/ae50fa6616f5a24ea2e68435f2dac7/1136_3IJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_3IJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/e4961bf3f7e6ba6e58074184763e0a/1136_4FT-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_4FT-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/12b332f9ffecddf255596ad8c149dc/1029_4PQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_4PQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/a133882aff1a27329fc14367dc1592/1136_7N2-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_7N2-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/4a98be77cc4ea7e7595e4683a795d0/1029_BDX8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BDX8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/4c4c328f21afda9196c7fda8edd8fa/1029_BE58-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BE58-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/f175bd8f577837e581cbfda192bd39/1029_TB8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_TB8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/c11fd2fb33a0be6044388ac3294aa3/1136_02J-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_02J-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/2c/f55e936316a366a24ddaf667a2c3aa/manifest.tsv manifest.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/2e05dac7981ab3123ec1b06d8314f6/659_eOm-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_eOm-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/843a1b434e4df28bc36574452cd345/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/439d7bba46aed78384e0d5dce7ba56/1029_TL0-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_TL0-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/890286ebc69309b376d841c2cbdf0d/659_b69-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_b69-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/8741ca5ffdf9e31a213db63674e152/1029_KBQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_KBQ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/cdf5d82bc63db0294ac09660b52d20/659_Yr-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_Yr-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/ea9455f8851ada347c45cc728a1424/659_7h-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_7h-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/3a07600d9e48db5a8e57b28959bff5/1047_CT-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_CT-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/4195b52d5b018df0825155672e181a/1047_D5-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_D5-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f33e1bd87c9f70985fa4ae76572452/659_dvY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_dvY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/101a97da0e8c8dc1af250b60d782ed/1029_ZNP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_ZNP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/b97660f4bd2646d952cb90c93d174f/1029_P7Q-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_P7Q-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/ddef3a024fb06349e064038322cc86/1047_IE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_IE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/906fd9225651343c95381f482ced43/1029_ILG-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_ILG-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/a94e46d21d4365da6bf75bc7d00188/1136_88X-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_88X-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/4f162398a3a2e4a3e0ed253bae78b0/659_cBd-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_cBd-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/32fd6d6bd54bc256887aebe99794f7/659_dAn-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_dAn-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/4fd97d2bbc24bbe87e546c301bacb3/659_kM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_kM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/1f81fa3ce860fea1eedcb4e6b70909/1029_VUO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_VUO-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/526264befae6bc466141d9cc19bbfd/1029_5VB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_5VB-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/83e3eecf3b7fdfa9845c03a82c95f2/1136_6DD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_6DD-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/363a37d8941dd23d84d7dd67bafa8b/1029_I9M-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_I9M-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/3423a167d12e17fe719c2257d23f7e/1047_G1-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_G1-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/93e660336b71765fc582e688830bce/1136_6IJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_6IJ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/0159ebf2994c7b3b37ebc689dcfcec/659_cAr-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_cAr-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/f9ae9e548e83fec7732fa2b9091542/1136_3NP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_3NP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/a5c0cfe3aad57fca40f0a44b984193/1047_BL-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_BL-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/051304be0a4e87846836186487f20b/1029_3TP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_3TP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/63ac4a150552cbf4a788a416cc8c34/1047_H2-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_H2-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/5c1b8a1df7b8dae02ed8897ac6a2da/1047_D3-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_D3-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/18fead332ef3aa4cfef5bf4834c19f/1029_687-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_687-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/05083fc070ccd920b32112ef0261ed/1029_IS4-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_IS4-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/fbdac32086c1af2def125827b48b5a/1029_WE8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_WE8-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/ca5e23dbe53404e8a27911d49c8060/1136_76O-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_76O-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/029979a31d1269ade930984a3c927c/1029_FP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_FP-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/fad9695c49da0cfd083f5d0054db10/1029_BHQA-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BHQA-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/fec11de045cccc0d6c3b786f4f797e/1029_BIBA-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BIBA-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/9758830f6124744f10373802de8c79/1029_ID6-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_ID6-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/82216714a1ea451c1c6d023352a894/659_cCU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_cCU-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/af1117ccf305e7a0e3d3453524e44b/1029_H59-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_H59-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/0b14bdbd2ae817ceea24d87dbe4736/659_eWE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_eWE-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/fcac85b913000b3a56e781b884ea1e/1029_QDW-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_QDW-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/4bf5adcd1ca90d4a4f590698010402/1029_B59-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_B59-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/d000c7d9a8cf395e6b0c25dbcfcbba/1047_BM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_BM-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/365f9a4e5aadb6eb899b119546c07a/659_d3d-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 659_d3d-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/34761ca25109b5576e8ad58e252c8b/1029_UXY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_UXY-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/c44e1f04f117ec721699acca41640d/1029_6UR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_6UR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/14563d15b38500d03504ba5c82dcb9/1047_KR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_KR-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/176c9718aa700058b78609183df0e5/1047_II-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_II-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/7d7b9da5cb23fad47abe3df3a72da2/1136_58F-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_58F-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/77b00c1de092e7267df86f625335e1/1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/140467485acc1614d4569767f7a1ff/1047_D2-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1047_D2-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/226b3c99c7e1a64e6ee4362f6518d7/1136_0HI-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz 1136_0HI-N1-BDNA-1_B23L5TMLT4_1_probes.tsv.gz")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (186 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/84/843a1b434e4df28bc36574452cd345")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/843a1b434e4df28bc36574452cd345 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/843a1b434e4df28bc36574452cd345 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/843a1b434e4df28bc36574452cd345 || 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/84/843a1b434e4df28bc36574452cd345/.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