#!/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/d1/b5f882ac242d99d774ede81b4aa359/.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/6b/c09a21e90e5f33967874bc76bfe6e3/659_eTs-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_eTs-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/070560bb1449e76df194c1db282c15/659_bGd-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bGd-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/0db7522db935fc6cb9db1bc3d92bfb/659_bOn-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bOn-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/57dfaf63e4e20320b911246a415310/1241_DG1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_DG1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/81341282aa6c05a2b4efa1660557f1/1241_M6J-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_M6J-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/6dfd3f12a142d80aa7cea443c164ed/1241_15R-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_15R-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/35f93b688d5fe3000d9fa842b508a4/659_cl5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_cl5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/cbefba50a78b37ec3f24ac47395231/1267_BK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_BK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/d9c4802c1d09880de12611f31edeb5/1267_DZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_DZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e986bdac874a8de2c4b40b60de265a/1241_IDO-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_IDO-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/edd27b130df2b02e35a329c874d4e9/1241_BJLE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BJLE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/4f54230ab9ec7ef9c3dbdea0cd28a6/1241_L7O-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_L7O-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/5e1752008212818828d883b2ae865d/1241_BIV5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BIV5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/91bb53ae1fe478cfca7fcd6fccbdbc/1241_BDD6-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BDD6-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/bbe859f9de58fa7c81063a0ba2613c/1241_BZNT-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BZNT-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/c9f3fe0f9733de61c02d1634b4d610/1267_EB-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_EB-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/b0ebf32bdaf5d0c88f85362e090eba/1267_EO-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_EO-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/d693ef3fbe98adf182d24e3807e1fb/1241_E4B-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_E4B-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/05e9730b3af6cdcaa726968299291b/1241_LPN-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_LPN-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/c5280a8c12cac14bfdfb124ba4f08b/1241_BBJ3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BBJ3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/128a538c3a702868f32648d73fdc61/1267_T-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_T-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/3119cb752fd0690af7339805f67009/1241_BD0T-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BD0T-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/0a91f474e233f1788df791343d33e8/1241_BAPK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BAPK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/899f5d9f7bfa796a68b470aa455845/1241_OQZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_OQZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/1f4588e62457039016b1b77845342d/1267_FA-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_FA-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/c6c6f871964c4ec0c7a25dcf677aef/659_n7-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_n7-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/733d6407f67e5d29cfcdd0b4f28d02/1267_ES-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_ES-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/fd55c1b4e449692cd9f8ffc4770a5b/659_e9a-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_e9a-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a378a23d21a508946507c77510c3ba/1241_3SE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_3SE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/0723bd2ec19f83d044e580ec1656ad/1241_BUM2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BUM2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/4aa8368a6455d83862a9ea76e80167/1241_PIM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_PIM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/5417b43316699115b4c287a9b4beb1/659_boM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_boM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/e1b7e2ddf5cf42b8ad35fd273466a4/1241_33Y-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_33Y-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/2bbc3821c5bd2674789eb846f390de/1241_FG3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_FG3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/15b81ac19138370b507549c896708c/659_eaQ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_eaQ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/7fa051e524ca4baa2524e77f67b336/1241_BLSX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BLSX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/58b7393b18238b494276d62813b5ab/1241_UHR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_UHR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/0738e2fa514be5a1e7e353cd04e0c3/659_ebV-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_ebV-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/05b44c9fc4469531bcce6444e1677c/1241_B1B5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_B1B5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/f9d6d3b23e4d995783a72f7d3d4967/1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/02bc9635c076a1f9793a203ffbc06b/1241_BJHR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BJHR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/6e5e5012ea5384b2b45852ecd15e29/1241_QV9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_QV9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/0af8982f7a54a3d923d86e5081fad5/659_eHK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_eHK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/6c4d8905d65300d7118dfb7aac36fa/659_w6-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_w6-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/056e01a480aa8bd7e96c2df88490a7/1241_B2HF-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_B2HF-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/8ea645b55298fdf90497b75a8e531a/1241_8FW-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_8FW-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/388b2bb41787bd4d002dae9d520d6d/1241_BGZE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BGZE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/5b08bc27754f8ed41fc42e51b3a44b/1241_DTD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_DTD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/5412a5f8c4d29aee7cbeb562b75ecf/1241_B3PP-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_B3PP-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/3b17b372a2297c9765eedf46b0b2f5/1267_D6-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_D6-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/73717f7b67068a28bf6269287e60fc/1241_B3NY-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_B3NY-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/43a2ecd9a79db7c080d49c52a156dc/1267_2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/738c04a43c459da5561707d81671cf/659_ddF-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_ddF-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/39b6ef7e41cdb9331b885b96eb5ae2/1241_0R8-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_0R8-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/a93c3ad04c8c1075853f2030f033ea/1241_T6O-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_T6O-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/62721bc08cacbd2b1f56eacc9f929b/1241_ERK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_ERK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/5802e86ef87f024ebeb989c581f005/1267_E2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_E2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/4a083af2d1158a97e9d8694fa2fc52/659_bOh-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bOh-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/88078600d8c2a0d13fb5c4da28e9c6/1241_BKG2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BKG2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/b51275af4c96f80690c2180c662d37/1241_IN7-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_IN7-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/c5a9d6547f64072e3657bf1b852edc/659_c8w-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_c8w-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b5f882ac242d99d774ede81b4aa359/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/18e8864cc2fd74f5d5e6a7c8a949dd/1241_NH9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_NH9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/dcc5a9e2bcd5f7eb5ac1b0905a3f52/1241_BZWC-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BZWC-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/ebbf85f09fe1d036b760f74d83cbac/1241_BQ0C-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BQ0C-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/c94b0b6a8f345925fd1a868f01797c/659_egZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_egZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/50190bc9ad661fdd14571cc074cf76/1241_BYI3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BYI3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/91288c39345151e946738a0c1b7c03/659_ewn-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_ewn-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/e34b16f897ac9da5e5869231feb6ee/1241_FG7-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_FG7-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/00ba9e222e0deb4d6a35a4ab68f07e/659_cCD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_cCD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/ca3a99aac6195e433d208822bde02c/1241_BIBL-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BIBL-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/86fbbb9e928afd2b0a2c802791572d/659_fap-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_fap-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/d88fd473de906fb66a747bfc04be3f/1241_BUKR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BUKR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/7c2ea97a8960220d6272af6c1e9a72/1241_B245-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_B245-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3e4dc28b0d2ee4ca4fb3a39cc93248/659_cvg-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_cvg-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/a170885ce7eeaec1336f41a14bb3b1/1241_FQ3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_FQ3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/739265e9614351be611493e09f25ba/659_cck-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_cck-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/aaa36cac7d5a7d56235dd4d6d95bad/659_cuv-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_cuv-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/9f824914b55f59fa2ce9e4823bbc3d/1241_BQM9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BQM9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/0a51b73f0538409f0f824a554cf7b2/659_dNu-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_dNu-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/92048bc21c8d522859a94c569c22f4/1241_S5N-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_S5N-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/39aff625eb72b3a8015f5dba0816a4/1267_BL-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_BL-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/f028f8fe57862454d8e35e044bcf3a/1241_QAP-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_QAP-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/77ced348bf5973b743b5437b8b1b1e/1241_BDGT-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BDGT-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/254ecef4fddb08d7f9491f4e0e1062/1241_XKZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_XKZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/cb56a4ff597d5c9d605d653a70f6a6/1267_EH-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_EH-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/555bb72f54cb86ff0a540a60478126/659_e2p-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_e2p-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/9c5a9bd94d300bf160faf070802c0a/1267_H-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_H-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/faa945baa10f1c6917b5e9d88394e1/659_dyR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_dyR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/85af5adb586a5af8f2a75e1f029a18/1241_TZ4-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_TZ4-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/3023c3142202ed09fdbde2ca79932c/1241_DI1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_DI1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/d9eaeed6e6335796d115d27aa8f027/1241_4V-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_4V-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/7f125b258a66ce079b3b853ac9605c/1241_J4L-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_J4L-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/cd287b2fdcaecf7fc3ab6028ea2148/1241_IYZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_IYZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/1ed6621db8ea9e6af5d691d2e5f1af/659_Cc-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_Cc-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/cd1edf8cbcf803ff380b327ee2e847/1241_R9T-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_R9T-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/95d8a27a0de6e5b9a4d5e2819a4b29/1267_DK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_DK-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/29e310be68998e3bd501c93c5784ad/1241_YFY-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_YFY-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/019322c831269eda67ff933cea8ef6/1267_R-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_R-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/a292ee4e38f6450b8a676a2fafda81/659_dNh-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_dNh-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/524c3357ad709ea3b598dfe291ed92/659_Pl-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_Pl-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/17c33581a116f34b64d1ba82dabaa9/1241_TBA-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_TBA-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fd702fea2da19e1a76e55ea3a0c5c2/1241_BV6H-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BV6H-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/3436108adc2d1b8dcbb1f9f856001d/1267_E3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_E3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/534facd41b7aeb0b1efadfae56bfe2/1241_RUM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_RUM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/4244f339be8c010277e68e68e74def/1241_BGI3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BGI3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/7f2cd82f7427f5d01fe8068e721ed3/659_b4v-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_b4v-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/66fa55dbd44d2b7c0187f97ec7244d/1267_DX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_DX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/bb8e5b3b342f3bae01cd3d8da00877/1241_RMW-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_RMW-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/fdca10c492c88310d1eef918a8eaa8/659_yG-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_yG-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/975b5ccbff7e764387c155bc892fb4/1241_F19-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_F19-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/bd261bb762dccab1c05b5a498c01df/1241_BPDR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BPDR-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/b771e604ef85f91ad1ebaee8f4109d/659_bT3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bT3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/4a6c1c95e3407f3140c83ba9aacc47/1241_296-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_296-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/3b32bd21830390732c4bf45ac476f7/1241_BL2X-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BL2X-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/768c14cbf2e7011b89eb6ef8d11133/659_dMH-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_dMH-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/cb57b53ace126a5653cfc558616f90/1267_EM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_EM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/fa2cde307c99b870899b380d15561e/1241_BHR9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BHR9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/521e8f5d99922f366fb2a9ed65270c/1241_WWM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_WWM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/73d62e1d9a2f5fb0013b64df37b258/1241_B215-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_B215-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/2e9a87269ea6ae99e6960c6d3a69c2/1267_ET-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_ET-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/833f092096010f1ac63a1f04e39a76/1241_G72-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_G72-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/87a3fca59f95e3902e796b28822e37/659_eGF-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_eGF-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/0c4b740081a4f70320ddb29a2df7c4/1241_BFJL-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BFJL-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/e790db7146fbc087a579ecaeb84580/1241_BGR2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BGR2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/4e/e30c7fbedb7bd7e611f4fad0debf34/manifest.tsv manifest.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/309193ece9a2fde6bb2012de441b62/1241_D1V-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_D1V-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/27bde2a35913869eb073dd9d3e736c/659_exZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_exZ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b5f882ac242d99d774ede81b4aa359/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/09233b135c28e2370c53f0130698d0/1241_BTQN-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BTQN-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/71566ac8932375e16ab16e3b9a5e03/1267_C1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_C1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/63e616cfe1b914a62dc7ca5a57bf9d/1241_BI61-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BI61-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/4d1f695a2aa9320df72455dfd455fa/1241_BRB0-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BRB0-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/8d9c6b5eb073c5580d29088dcc75f2/1241_BUFE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BUFE-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/c8cc7deb7bff6ecfabb90d53cc17b1/659_ein-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_ein-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/15303c0b5cb71d647870b93e50d472/1241_BUK5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BUK5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/a5ca1df164658c06894c87263a06e2/1241_BTVD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BTVD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/80b9201fd85152a7bcd73138d52cae/1267_BQ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_BQ-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/0a658065faea25c3939f05da308176/1267_C2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_C2-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/fadcf9e58dfdc45d32f59aa2e21d34/659_8w-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_8w-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/bdb6c905b52ce894dbc5190d25b403/659_rr-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_rr-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/4fd62d33cb3c3bb01c52d434810237/1241_Q4P-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_Q4P-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/cbab52046e78f2c09773a59538aa65/1267_0-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_0-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/5e8f95eb7296ba02349dd28a5507d4/659_cYX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_cYX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/f928feda252c88ab7df87c23cf2de6/1241_BHCY-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BHCY-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/ed82567a7c3af3964b2bb4c5f5ebd6/1241_BWG3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BWG3-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/90604cb7e23118e325dd9a86368452/1241_BC3K-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BC3K-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/074fd13f794dae31a0db57ecc53d5d/659_bV5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bV5-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/5a55c31da2847d8a0902c5e316aaa3/1267_EN-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_EN-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/d68eed0ebb878bc2bbe066c651277a/1241_BDC9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BDC9-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/c010307d6c4adacb6600ae912cc726/1241_6R0-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_6R0-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/a88ca8a9b1042ea46647ef3a112d2b/1267_CI-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_CI-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/bb6c1802dcce8bb5cc29d67bde4a9e/1241_BWD8-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BWD8-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/d06c186d94ce151b8e467c34685a46/1241_BK2S-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BK2S-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/b70d4df93e6e35f57febb21ca6c4d8/1267_BD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_BD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/7edc57238e2733c6ff0672e1b5b40e/1267_CH-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_CH-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/5f9c233a7243e0f4594586dda63b17/1241_0EP-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_0EP-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/d35902b7e0915765eb749d1d59660e/659_bqk-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bqk-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4ce1ed8d3c113eacb360c4be481866/1241_DW4-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_DW4-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/a41a911f38b172dd2c619b339a4fe7/1241_YAG-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_YAG-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/b56186686af3dfce1e4b8b2c0e1e5a/1241_BXHM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BXHM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/5d26f8446fcbbcc96538204f9a74ec/659_bXS-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_bXS-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/b89093e41e354af7e6fd84245b119d/1241_F1Y-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_F1Y-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/871bbfdc012214250cdfd3bd6aa00e/1241_QWS-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_QWS-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/2e14244dc6bf4ff6d8a430c81d39a0/1241_731-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_731-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/579b9ec9b12c83ecb14746f287a868/1241_BQCI-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BQCI-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/a06cf4c5a5c0f8b050dca8de884006/1241_WRM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_WRM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/4ebc0b2a01d416554b0dbdcf36fed6/1241_BVJC-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BVJC-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/2fa5894bc0e59f77d28d27e3a4184b/1241_BBKM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BBKM-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/e53c7db9f40086118d6c117912eeaf/1241_BP9P-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BP9P-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/2fdd846510ae226531dbe4caa73bb9/1241_VY8-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_VY8-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/4ec33ee95f66fbaf79dcd93b359f73/1267_Q-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_Q-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/ea921edd8ec6b73229df3c8ba74b56/1241_BD4M-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BD4M-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/2a1cc218e2c4db41c6b2761dd0ac48/1241_IHX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_IHX-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/d1dcd02b2a8c2176bb8cd8afcf9764/1241_BSFD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_BSFD-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/7bb1ba9cb7573d6a93c789461f2a0c/1267_FC-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_FC-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/747a508dc5894f1b11ef49631d84eb/1267_B1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1267_B1-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/014bcf9648ce6b63fe4f5ae1829888/1241_JH4-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 1241_JH4-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/302ca7aa2e37201a6f4a8d2daea917/659_dz-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz 659_dz-N1-BDNA-1_A23TNVNLT4_1_probes.tsv.gz")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (179 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/d1/b5f882ac242d99d774ede81b4aa359")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b5f882ac242d99d774ede81b4aa359 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b5f882ac242d99d774ede81b4aa359 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b5f882ac242d99d774ede81b4aa359 || 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/d1/b5f882ac242d99d774ede81b4aa359/.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