#!/bin/bash
### ---
### name: 'GERMLINE_CNV:ProcessBatch (1)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/sarek/altera_cnv:0.4.0'
### outputs:
### - 'counts_1.parquet'
### - 'sample_metrics_1.parquet'
### - 'ploidy_1.parquet'
### - 'B23H2H2LT4_1__sex_calls.parquet'
### - 'B23H2H2LT4_1__sex_calls.png'
### ...
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/4f/da1360e1d533b3c711d4b906ac3918/.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/d3/de46e1e4afae22ef9997619d689968/NA12878_c_0002_gDNA_0003_A23NLN3LT4_1_counts.tsv NA12878_c_0002_gDNA_0003_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/f883a2ff39b60f3fc3ba3017663eb5/1136_43M-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_43M-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/977f1382fdf9da1eace0525d70aaef/1136_5JJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5JJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/1c53b8d41f3b6746e24a01bc1c024e/1136_7DI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7DI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/5c3db40d041622982431069493373c/1029_4BR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_4BR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/af76a6d427faf8d94b90d78e462263/1136_3RX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3RX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/5c7aaf5cdbf81d0f3660d35c57405f/1047_KO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1047_KO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/f23ab21c4649eb42f8b6bd6019f9ed/1136_2QN-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2QN-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/f0d842e1e714841e02a0d4deff2d1c/1136_6KJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6KJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/4db3491e9f36ad79373b58b268e026/1136_7LJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7LJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/3be33ea7869a7d95124e074f35bcb5/1136_62T-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_62T-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/74a724a59901ce8fa94253454c1768/1136_8DR-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8DR-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/ec9dda758ece65327df7ad6bd05f57/1136_0DK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_0DK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/9b88508bd154e5c3559dff86c1c9bc/1136_3ZY-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3ZY-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/38d823ecc1820183a5e95b43641da7/1136_7W9-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7W9-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/ff49cb6ba98c577939e49299fb8eed/1136_7VX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7VX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/ea464fe7b48b131dd31ecf7a983221/1136_3PA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3PA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/f87ff409474ac38ab3c38d5fdde57d/1136_3CE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3CE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8db279e4f5f9158fc76b8107571cbb/1136_8CP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8CP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/a9419627b48740954f46b52662b146/1136_53-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_53-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c95db68f507837de9375b8bbd1d6c4/1136_02T-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_02T-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/c8f40e477f0f2a773a15c8c60e94d3/1029_BPPR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BPPR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/90ea75255c14f3dd0e120c9d584d51/1136_49W-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_49W-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/06cbf42b31389520ff072539419fad/1136_3QJ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3QJ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/325ae62449447d1cc2333cd72240f5/1029_BOLC-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BOLC-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/5a8ad9b35772df2d1b95b22d9b2111/1136_4WS-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4WS-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/0dc7a05f2df682d0cd050528249148/1136_7U7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7U7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/317b67c3dbd96fcd9fbbdebba7cd10/1136_70Y-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_70Y-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/8a522a59bbdcf5d2739618adc4c0d8/NTC_0002_0030_A23NLN3LT4_1_counts.tsv NTC_0002_0030_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/5b1923c8bbcdfa0d2175e70168a233/1136_8ER-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8ER-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/01c0ced7affdb00cfb9052de06eaa4/1029_IE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_IE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/02b9db13813c378dc1b20826e0eba7/1136_50R-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_50R-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/11df2421b48706947a428440a4024b/1136_6BT-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6BT-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/055362fe354e50ac1dbf7d5884a9d5/1136_3XK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3XK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/7c751f195e2608b5a8e399234d9af4/1136_4XQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4XQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/24b1a16ece5ab3422ff400c2d75f32/1136_5I6-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5I6-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/f94188dfe4b081d7dbdb7ae3181ac0/1136_6S7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6S7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/dc8af543599374feaa89ce43cc0389/1029_BEA3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BEA3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/b870ee15b22473a7806bfc5d7e49b7/1047_E4-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_E4-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/88b37e59b02589691fc037f1f286fd/1136_469-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_469-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/b2ab971dae78e0604c29f93aee04a6/1136_584-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_584-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/ea755e4e5b8056e445244c9e426729/1029_BCT5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BCT5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/47fa71c4d90f8aab837c0ab331288f/1136_1GT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_1GT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/6362cecaaf7faf535fe479b0f1ac71/1136_28I-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_28I-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/8c38a580e7696ebf099e59f10441ac/1136_8CN-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8CN-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/ad5ee4bc38d8faf5dc087bb3e42fe4/1136_6MU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6MU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/d8ebc680860ae495cfd2403454f587/1136_1XP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_1XP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/f531b13b22871415a09b9bb8e7513f/1136_3PB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3PB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/f167795780193f595e2769491f5294/1136_158-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_158-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/27b43ff32dec72b39ea291532f4741/1136_50I-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_50I-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/5c064098f4af3ca325258179ca6f53/1136_268-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_268-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/3ee029be3f2541076f55470506e55a/1136_3XL-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3XL-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/a7b37bf1caf503d12cacf6573e670d/1136_4DX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4DX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/c2611fe88d5fd303380e74203c3679/1136_4ZW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4ZW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/3daaa91ea5256ef4a88faf681bdc5c/1136_4CO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4CO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/6080b142e27670974644a4a41a9861/1136_6H2-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6H2-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/53bbe4db7fe38dc900fa67a3386423/1029_9N5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_9N5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/43480c314d7ee8d92b69c569c1f3a5/1029_BR2G-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BR2G-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/e8287b6e27bc5e0d27ca80f0d4b902/1136_0YE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_0YE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/9014c0aa3986d7b4aad8bcc6b58d46/1136_6EX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6EX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/2008b99fd1a4d17db6447a4eaae2ce/1136_7RL-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7RL-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/af5482aa0daf4fd5042021ed7c47b2/1136_60V-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_60V-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/f7f5af727eb810bbdf0dede9e35094/1136_6YW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6YW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/11497c16033de9786005a73e896be6/1047_IR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_IR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/56a9a7ee68514d3ce500fc2b5b55c6/1136_4UJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4UJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/3fdab11ec58aa08526162f20a88428/1136_4UU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4UU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/fd0b3fac4550f6d253d28082cdee8a/1136_5ZD-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5ZD-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/cc4edee2c425d9eb07e02518a70c6c/1136_3NB-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3NB-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/17517735a48291a6fa898d8b9bbc28/1029_BAGZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BAGZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/e90e40213ae5cefa77cc588d4c75f9/1029_I-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_I-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/7bcec8f132562366f9d236e54568f6/1136_3A-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3A-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/fcf18c1af86cb09c6e2697781726d0/1136_51O-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_51O-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/071f28d63213769146155dccfd189e/1136_4Q0-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4Q0-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/62d3107c0c5f6912de0ff233c4606d/1136_6K9-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6K9-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/513d47ca68cf5d97bcec31dd50c25a/1136_6Q7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6Q7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/d1e9944b99303d64a577ccd21dc84b/1136_50N-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_50N-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/0efbeb5a45fe76f3fb8d780e8f1e44/1136_5UH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5UH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/c06f13ddc90da7471ff039a5d43db7/1136_5O7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5O7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/6f8f7e0bf1921b270763bf022403f0/1029_BB3R-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BB3R-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/be23e845bc71f38dc00a510f4bacf0/1136_7RX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7RX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/ac522b0cc714ea88ca22a1437e92b5/1136_66R-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_66R-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/1b1a7f5dc983923b728ea8b982b116/1136_431-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_431-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/49ec217463fd00303fecdac74018ed/1136_2DK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2DK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/c8fb46f42194f370a0a2f03b60adf6/1136_61K-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_61K-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/45a2e9b95f99e924d758d8fa9e290e/1136_02D-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_02D-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/6f7b9f3121778676f373f88f2187ae/1136_2R3-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_2R3-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/7f6deacf660bb30fd903ad225b5693/1136_0YT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_0YT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/bf216b8347c327adfe87821d2aba6d/1136_70J-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_70J-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/0c2aa97c08cecaf251e76fc248721f/1136_3UV-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3UV-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/23257d2477e27549b551195d59e662/1136_293-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_293-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/f7b1d76239d5b5b70cd9baa3119f6d/1029_SPM-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_SPM-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/e381dc33d53e7cc9233fceff72b76c/1136_73Z-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_73Z-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/9eab3e8eedb556644bae333f225073/1136_6N0-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6N0-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/55a2bd740bd41e4a65041fc726804d/1136_4JY-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4JY-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/bfe4a46a3fd6fdb978466af8614870/1136_2B7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_2B7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e0f6ebddd87eab061f9fd9834c2659/1136_02P-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_02P-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/389aa174a72a9607e87db0f311a823/1136_031-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_031-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/dc2b319348d4ff15223e6b94829944/1136_5HE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5HE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/9d9336cdad05440020b0c99daf4de1/1047_CQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_CQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/a49bf0e71c8d10b69d889ed4a678c3/1136_4XU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4XU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/ec346126186629e79fcf60363a606f/1029_J3H-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_J3H-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/35d10243c2887c40dc196b76b6374b/1136_2CW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_2CW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/22a548c8381a5689b48d66bd44c9ad/1136_2QD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2QD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/210545e56e61993f371859bb426fd2/1136_08Y-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_08Y-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/ec276ffc286d0df67d8e0ada2eb795/1136_6IS-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6IS-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/efb80c3cf6079b28e6589d38dcbd2c/1136_57Z-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_57Z-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/92c156940fa9d0fe84c5530570b056/NTC_0002_0029_A23NLN3LT4_1_counts.tsv NTC_0002_0029_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/1bf5ad84775a4929725c1f9b3fff5d/1029_II5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_II5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/7ffe3e4c9aa8bd3daf43b9dc3c56e9/1029_KU7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_KU7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/b89269191990963c9572aba1af7f05/1136_42J-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_42J-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/de36072322b5c22dc7b6033bb9ea8c/1047_BW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1047_BW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/a9df270af3be080bc391c2f5bd41bb/NA12878_c_0002_gDNA_0002_A23NLN3LT4_1_counts.tsv NA12878_c_0002_gDNA_0002_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/feee100d5e8a4c6ddaa5dc28e6dccb/1029_VUY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_VUY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/9f59b9163f24cf34d462a05288768b/1136_4FP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4FP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/d8661e569fbc9624e899fcbb134037/1136_3Q8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3Q8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/2bea4c5c9e619a965901e9259e5be8/1136_3CK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3CK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/55464b13264dd4156377bbc29204f4/1136_3PM-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3PM-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/d7b2993339743ef107b8222aa7ca4f/1136_8E2-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8E2-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/8e37a4bf4fc3ae5c3500b78ca21557/1136_1UW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_1UW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/80ecc6adfe71df3b26a3d2186f2af4/1136_64N-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_64N-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/64ea38572241db5006602c65e1281e/1136_20-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_20-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/a6c6471aefd6b588be635f8303e053/1136_06M-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_06M-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/3c687d49cc1d0509777ecaddcceeae/1136_6F8-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6F8-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/525e78f762c9a715d6720db965c34b/1136_207-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_207-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/7b8aa492b09c46964cedbff2a08fce/1136_7OX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7OX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/edd99a6e5c6a403c4ecb126bed3f62/1136_6VC-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6VC-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/c99445d8780d527b43cae0f3c18a33/1136_2L1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2L1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/02dded03017d80fee66d7b3650ff6c/1136_5BU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5BU-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/3ea6f4b44efb28689cb626e31420af/1136_7Q0-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7Q0-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/ba91c2cfc0f66980c80f4c7ec05c22/1136_4D8-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4D8-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/e36e35d37b7c51e42132bd56958957/1136_5X1-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5X1-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/8e2e904294f2e82c93b2877dc0757b/1029_MEB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_MEB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/28e7081da462cca3b8c9fbf566fc0f/1136_13S-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_13S-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/c13c8baf9b1f2b2e8de524031670a9/1136_624-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_624-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/a4c33985e6234c4e094ea3dff4df23/1136_10O-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_10O-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/a4920096eefa32d68f050acaf3238f/1136_7BQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7BQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/a838213a0f0a637af2847e540891db/1136_7YE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7YE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/8821210e7dd3b00c729980e2266166/1136_3XT-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3XT-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/49a3191ad058cb6654a0b5cc7f8c65/1029_G7Q-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_G7Q-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/17bc8dc37e5a5af487bf16017347da/1136_6TW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6TW-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/56264789b7788f1cdc040fabdb94cc/1136_2QO-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2QO-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/78b4f5ba24baead629035bfe561414/1029_BC2W-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BC2W-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/b6db060b7498e1434b5f4d412cfc18/1136_3LQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3LQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/3c740c9501b51947452da225e9e571/1029_P5J-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_P5J-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/d5bf46b950f211a327f7d9285910a6/1136_3U0-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3U0-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/e53e62cee98750708ca7892f3c95fe/1136_0TI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_0TI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/2878528686975a41fab6a631dc2513/1029_IVB-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_IVB-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/dd1a1b2dd4f5fdf68313891f7af1b2/1029_BF7W-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BF7W-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/83467e5d1f0e60e1b491ec050a6d22/1047_B8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_B8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/e182d527d9522d5b759b5c8a2af441/1136_3G2-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3G2-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/4db8486d394a06fc5ac99e65fb37d1/1136_7Q2-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7Q2-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/66f28369747077b212ae88ee258d93/1136_4XV-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4XV-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/d51d284490fbfe6095f0a1d4c8ccfc/1029_X42-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_X42-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/8fec9502616db6b8d37e2eca267131/1136_0VK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_0VK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/0c8763966cf241d6cdc047c7cb1715/1136_17K-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_17K-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f3dc6b2d4f8c7fb521b1189c1aa020/1136_1Y1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_1Y1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/074933848d9725abc0b1257c94b3cf/1136_7KK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7KK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-platform-sandbox/platform_projects/altera_cnv/altera_v3_panel.bed altera_v3_panel.bed")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/253e9afbde46cdc6ea6179e09ab920/1136_57T-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_57T-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/3605b883150cfed71f558f2fef3570/1047_CH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1047_CH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/9ff50b2752fc6b95dfb7167238a202/1136_6G6-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6G6-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/d83da74cd6ba228763a5c6887f0c87/1136_74F-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_74F-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/5e36722ba7b6fb78f4c22d3edd1eea/1136_6VE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6VE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/4336ab7478bc0f65c58fda8421ff97/1136_1V9-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_1V9-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/85c57e4fd9d5c355dc727519b67072/1047_HS-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1047_HS-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/b772b0375f843cc6c72458baf33ff8/1029_N53-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_N53-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/5e436ac683736c34be105d321b18e4/1136_5J7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5J7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/10bff27e4b3e0a6786986db24e022a/1136_7W6-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7W6-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/2173e8c0dfabb15a7122cb6fac6ac6/1029_BMAA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BMAA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/a7d64750f17ebd11fc6d3bb215b210/1029_BJVV-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BJVV-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/af2c746b6faab53be3cf7dfcaa1088/1136_3FD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3FD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/640e07c7dcac0c6241291fc57d18ba/1136_2YW-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2YW-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/6f84a7ad7417ca1f9b6b23f18886b5/1136_7Q4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7Q4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/46de5e516f09729dccea665061db37/1136_2WO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_2WO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/756c0a38797405130d6a8a0f411ded/1136_5KM-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5KM-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/fb1de250c6d4209d7e3bc2df61e4cb/1029_HST-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_HST-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/75c15e447ea956d015ea89722b5c4a/1136_3WR-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3WR-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/85741cf33499dbf8df91bd3b94ef47/1136_6SH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6SH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/4888042556b5b98fa4af5a044ac71c/NA12878_c_0002_gDNA_0004_A23NLN3LT4_1_counts.tsv NA12878_c_0002_gDNA_0004_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/b07075f4d7a6b7a56625a2dd63c4a4/1136_5JI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5JI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/776e5286bdc520a6ef024b778437f5/NTC_0002_0026_A23NLN3LT4_1_counts.tsv NTC_0002_0026_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/92e42acdafd7c59f1422870094b95c/1136_5PH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5PH-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/2db643a631c3e6efa62ad947cc609b/1136_7GE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7GE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/e547159ec29159c1938bd2f4b096a6/1136_5DG-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5DG-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/bef9bb1efca767793ac6f033d5816f/1136_33Q-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_33Q-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/a03aa9a34b14d561ec171bd793a477/1029_BH1I-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BH1I-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/43cf5046ab3896b04ea3f2bd879de2/1136_6ES-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6ES-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/836e24fb6b9097c77c16e68b6c4810/1029_JU5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_JU5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/12290996e2636d061546c96813dcdc/1136_3SI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3SI-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/212b113b8fe3965f4306a072b75767/1047_B3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_B3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/6f85ac0796bc3cfdedc84adcbcb8ce/1136_6AL-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6AL-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/4062460b1f92542ae9595aa0015451/1136_6RX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6RX-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/e7fa4fe617994498f85b74a60292ef/1029_K91-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_K91-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/e2c24b93561bc620f48c3e2df424cd/1029_9US-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_9US-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/c9a3d64b9ce25a34717b4dc398cd7a/1136_3HZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3HZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/11f956f407d0f575af040dc8d5ef50/1136_3GO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3GO-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/582c51f80aa9c2a0fd24b1826ab0c6/1136_0NS-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_0NS-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/8540012db9e6b9cc99ee9fe9eb32c8/1136_7AK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7AK-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/20def5c23d5df2110f1775888c3ac5/1136_59B-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_59B-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/b0957a2ebde71148e49b401fcb96b7/NA12878_c_0002_gDNA_0001_A23NLN3LT4_1_counts.tsv NA12878_c_0002_gDNA_0001_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/57515d88b269f5ac1b6598f2badb2b/NTC_0002_0025_A23NLN3LT4_1_counts.tsv NTC_0002_0025_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/a2bc66bf7411095b114839db4291f9/1136_3Y2-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_3Y2-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/9041da6b236caf458ef88371ae5ac8/1136_3WP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3WP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/3747984889aa00c28dcace0b235491/1136_4NM-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4NM-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/e5df3a27226b0188a1468ad175f294/1047_MY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_MY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/a953527168e3302f3030eec576a3fe/1136_7W4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7W4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/272e42ed8ba74323f23933ab2b4833/1047_JJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1047_JJ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/740672231530e0f2ca8e29ab8c0b1d/1136_2YQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_2YQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/a0fcbe24517853dcda4726ff7841c7/1029_J3B-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_J3B-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/ce8417b0deedf2226c7c38355b0a39/1136_6QB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6QB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/38234566927ba07eab74601eb733c0/1136_5GA-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5GA-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/76bc324a41a8c1e2a2b255b6f0da45/1136_4S4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_4S4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/42a1fb34225b6dda5f7ab6439e3468/1047_IQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1047_IQ-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-platform-sandbox/platform_projects/altera_cnv/altera_v3_variable_regions.bed altera_v3_variable_regions.bed")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/09c5d5d3862d425f9934b463c43e54/1136_3J-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_3J-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/d5b0c78235b25c22b2e6a69a1e3eec/1136_01L-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_01L-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/cd/ab3dc34c234d6dc84796380231432b/germline_cnv_input.csv germline_cnv_input.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/768aa72e80a0de4102f098493c6e1c/1136_62D-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_62D-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/15ba87aa0af8679f9526060f666cb5/1136_562-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_562-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/9573086481582e214a0bdd602f6cc0/1029_YES-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_YES-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/10a7a14d82554b7668dfb2af42cb68/1136_6E4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6E4-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/faea587bc52c8e75d16282b6d69a72/1136_7OP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7OP-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/57bd3567bf2b10f0228e8f81e2a626/1047_FF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_FF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/ca8f8b37130a99e98de10db34aa3d9/1136_2XT-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_2XT-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/4eca25562f446979f571a6dea2d9b8/1136_89G-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_89G-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/c432882cbdaa66f3319232cb2c09d0/1047_CL-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1047_CL-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/afa6bb029eaaaf07b638fed794b6aa/1136_56S-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_56S-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/3c3c538a3f9a21c226f432632df28b/1136_5ZB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_5ZB-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/dbc2a9f8daefe84f365376eef0b926/1029_QZF-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1029_QZF-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/bedbdd7efff662980608ce6d59b60b/1136_70A-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_70A-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/fdade05eb16b574930cac5b1183130/1136_82G-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_82G-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/327078642c98e17ade36cf6e1c69ff/1029_G6U-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_G6U-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/8dfe38b1a4e52b43c381a51ec32560/1029_I90-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_I90-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/b3621f3eaa8ab0ec60c0e8ca199740/1136_2WD-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_2WD-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/56dbf9d8de633f0af0441bac27ad10/1136_6WC-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_6WC-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/09be0b8c56f1eaa3f5e2ddca390c64/1029_BCL1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_BCL1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/2f69be23e45586b1a3069834017729/1136_8E7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8E7-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/0b5f8f91edecd6f1b5ebb67e8d0aa9/1136_8BN-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_8BN-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/c87c1de2dffd34dfa4f5627c20253b/1136_1JF-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_1JF-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/06dde3322f4cfde3fd6779f1f285f9/1136_7CE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7CE-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/2c1e11d5252e59a9404d26eb305149/1029_HTR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1029_HTR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/8945028daa997bb04711e5a5182646/1136_7C1-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_7C1-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/1a55bfec71f9c74c01632011cfe842/1136_76Y-N1-BDNA-1_A23NLN3LT4_1_counts.tsv 1136_76Y-N1-BDNA-1_A23NLN3LT4_1_counts.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (245 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d counts_1.parquet sample_metrics_1.parquet ploidy_1.parquet B23H2H2LT4_1__sex_calls.parquet B23H2H2LT4_1__sex_calls.png" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/da1360e1d533b3c711d4b906ac3918 || 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/4f/da1360e1d533b3c711d4b906ac3918/.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