#!/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'
### - 'B23KGCJLT4_1__sex_calls.parquet'
### - 'B23KGCJLT4_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/3f/b84e098cdd503ac274dd4fbe4f1c44/.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/2f/d6b5133485b3998f8a2bf49c312965/1241_BVMK-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BVMK-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/26646cdfc47379e702b057bc9289ab/NA12878_c_0002_gDNA_0005_A23TY32LT4_1_counts.tsv NA12878_c_0002_gDNA_0005_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/83ac2017369233fd97ee6167fb382d/1241_BDC9-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BDC9-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/19aede1dccff8ad006d8672b53325a/1241_DTW-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_DTW-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/5d053c14f19a77ec961379c1861d72/1241_BIV5-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BIV5-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/96f4b3a0e81ac7f4aea571756484cc/1241_F1Y-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_F1Y-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/0eeccbaeae8dcdeb82e6b1cd1d626d/1241_BXXW-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BXXW-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/367e091b3b53f7ea94a1cd41c2918d/659_btY-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_btY-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/51baa313b6920112be1bba3d2917ef/NTC_0002_0007_A23TY32LT4_1_counts.tsv NTC_0002_0007_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/96e401c7d68b780fb6e6761eb8830b/1241_BYI3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BYI3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/895ddd60736414e92586ad598a3e52/1241_NID-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_NID-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/4db8f5761a301e47e9679fffa2a4e9/1241_HFU-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_HFU-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/804dac3447ad072fd459f61883eafb/1241_CI3-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_CI3-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/d1b0be0c7b565224c9602548f9ec67/1241_CN-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_CN-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/334da70c15f1e48a0b6748a56583c9/1241_BTVD-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BTVD-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/837b8d8a42adf1af5a1120ed067377/1241_KP1-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_KP1-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/eeaf9a1897087526bcfb109f46b6e5/1241_BWG3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BWG3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/3b5aa29b0f56d76a0810ba444853b9/1241_BSFD-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BSFD-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/d37755a77c8b1cee888fd6dc77a142/1241_BZWC-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BZWC-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/2d2312e88b6d46cb457baf2bf098a4/NTC_0002_0037_A23TY32LT4_1_counts.tsv NTC_0002_0037_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/546e41bac0d26a0f7fbd13c3c8b06a/1241_BXHM-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BXHM-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/2ac089208da9a390de6d7b183fbfc3/NTC_0002_0030_A23TY32LT4_1_counts.tsv NTC_0002_0030_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/854ba616cdabc13643abc16d1ef12a/1241_QL5-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_QL5-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/60f76eb3fd597d1cbee003ee67da11/1241_VWU-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_VWU-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/c15737b8100a130670f1f1bc58f74a/659_b2o-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_b2o-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/6b2b6c112167156e60a7cce663cf8b/NTC_0002_0035_A23TY32LT4_1_counts.tsv NTC_0002_0035_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/1de92a355f1d37854a9e6baa53da5f/1241_BSJ5-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BSJ5-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/0b871b58726558c1d8e9c2e70f3fb9/659_ehU-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_ehU-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/462ec12bbce67f3fcafdf5ff9b33ac/1241_ILP-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_ILP-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/08a278036ec98d48f5d8b7e272d03b/1241_BWD8-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BWD8-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/e49a6cdf437fb154d7e70b5affb897/1241_BJHR-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BJHR-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/7339afe7cf0e2e21836868d6d80bed/659_ND-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_ND-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/f76110cbd3d9f2dd42d8b01f0dbfb0/1241_BFJL-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BFJL-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/dc5711fd65934db5601d1e6c0e8745/1241_TC0-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_TC0-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/64caa2a6caf32199a848703281822a/1241_4V-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_4V-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/e8ea0b6b24c9e9c4b50ae4349ddd15/1241_0EP-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_0EP-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/10b6b4475d25d2d6150a2a9dc8330a/659_eAi-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_eAi-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/31ac7f0b50e073eea5cee981685d6d/1241_BVTH-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BVTH-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/7cbc5b1826e6e65ad7f1265bb10e22/659_eci-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_eci-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/ba1be177fe2ba5773c681686e38d79/1241_SSX-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_SSX-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/0b1bff5e5ff269d6bf827291875e0b/1241_RW4-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_RW4-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/b37f4aeadd86db13bab454ff0f5b6a/NTC_0002_0039_A23TY32LT4_1_counts.tsv NTC_0002_0039_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/4e10d7e683bc6ba99d932ad9876b77/1241_BZNT-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BZNT-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/2575f53a913d190f8f4eb926e7aefa/1241_BQCI-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BQCI-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/41d532c4f5a1ceb7865116b3111709/1241_BOQK-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BOQK-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/d22acb9a25efc486836f1361f71487/1241_BRB0-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BRB0-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/3381bd35f896486ec65461006c8038/NTC_0002_0045_A23TY32LT4_1_counts.tsv NTC_0002_0045_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/6e0ae094c196fa5110df0d50543108/659_eK7-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_eK7-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/e3eb0eb13b62afcb18c7fbfb4bbd1c/1241_BU9N-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BU9N-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/9d50e346a81234b411946548a629a6/1241_BI61-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BI61-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/8221b17c40ab8a287ed05724bd38d3/NTC_0002_0017_A23TY32LT4_1_counts.tsv NTC_0002_0017_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/c89f28b3e354925e3fb977e4e6f8c8/1241_BDD6-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BDD6-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/05709fa343229712c7cc32812596ca/659_b2G-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_b2G-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/10323e87ec54f0f7acdabd9050a219/1241_V2H-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_V2H-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/4d3be3808eb43ee9a4cec6f26ab3a7/659_wS-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_wS-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/a880ccb3e614722fd959f021af2b2e/1241_ZEX-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_ZEX-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/ec4f71af9969d60af94856fcadd3a5/1241_BGZE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BGZE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/74377c4c64b706bef12b64ba961a36/1241_WRN-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_WRN-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/4ac0a3ac472c07ded755e1b52bf176/1241_BXO-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BXO-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/545f74b372f9031ce69f61cdd24818/659_jS-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_jS-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/86d9a4117963e2a0ca8370de5484d4/1241_731-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_731-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/4872f1b6b210391a06c3c56d5ffa9b/1241_BBJ3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BBJ3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/b9cf600385d5510e8640150ed98666/1241_BUX8-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BUX8-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/6a68f9504f093cfb98212cb3b51ad2/1241_QH5-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_QH5-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/048fb2ce65ba3645bcd6dabb2b3ad7/1241_BUFE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BUFE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/c17e4fb0870a1f419745f000e448a4/659_e4m-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_e4m-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/4c0397f0a3720c642a7949327357b0/659_exw-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_exw-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/99a7741e67d2bbb0eeb74f9ac93547/1241_HS1-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_HS1-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/6e220ec7d014ef53a7537fdc6c03fa/659_cJ6-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_cJ6-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/3871f2482b1aebc63d0e984f62cc15/1241_BD0T-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BD0T-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/13d88f13b72909ac6a68893649f66b/1241_BD4M-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BD4M-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/365b2444c4f245d9d6efcafafcc403/1241_BIBL-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BIBL-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/1e284c6ddcc7bf3ecbb18d8808c6f0/1241_15R-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_15R-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/7a038a3e8d49e9cda43ea501a84140/1241_D1V-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_D1V-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/a71755be7659715de7d6d170795d7a/659_dyZ-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dyZ-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/78aa2884367e39ea79a4d38dfde919/659_dNQ-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dNQ-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/64d9050cfb5320ff55f494f4c4423b/1241_BVPH-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BVPH-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/abc824b5f2b5a8103c6460a3095cd1/659_cQZ-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_cQZ-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/42dc5dcc7d0cee586434e95cfb05ff/1241_QNP-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_QNP-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/789014134633e3e9ae5cb2d1d2a3b9/NTC_0002_0028_A23TY32LT4_1_counts.tsv NTC_0002_0028_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/2e541b78a8bda477e66406531aa3cb/NA12878_c_0002_gDNA_0006_A23TY32LT4_1_counts.tsv NA12878_c_0002_gDNA_0006_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/5f417d3e37ca1ab5aea5d863f016ca/1241_BW0I-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BW0I-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/eb497d1e9353ef8712fb87af24c925/659_cD2-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_cD2-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/2891451e31064621013279d49465f2/659_d1e-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_d1e-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/79b4a82fbc08bbf18862d75db9bbe0/1241_BBKM-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BBKM-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/29280b3cffc0a2805f8a579057eafa/1241_JHS-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_JHS-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/ea4dfe783df9cb84702ea335d14fdf/1241_BVLB-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BVLB-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/cedb6b3ebd998379cb8141acc9dd62/1241_USM-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_USM-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/865a1a67e695f9f43d0d9105edcb3f/1241_RZE-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_RZE-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/b37247dd5b75b5cbbec5262b53bdea/NA12878_c_0002_gDNA_0001_A23TY32LT4_1_counts.tsv NA12878_c_0002_gDNA_0001_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/bb12cd52a455645e54ba1f2fd184fd/1241_BDGT-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BDGT-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/6785189558dd80516ceae17ca4cba5/1241_JM9-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_JM9-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/b2385de2f800d7c19b158541948beb/1241_GE3-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_GE3-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/c92dacd42bd3ba56236bf554256df9/1241_DI1-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_DI1-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/b5f7a7f93f47f8bce34520fcae244c/1241_B3NY-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_B3NY-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/1375b62177611e2dd123e51bcb30ff/1241_F19-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_F19-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/4db55c41592554446cefde34a0701b/1241_BPDR-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BPDR-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/b207ae571766387367e1b0d358c558/659_ebq-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_ebq-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/9a17bdf9e4f77a587fcdc511ef58d7/1241_BGR2-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BGR2-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/31f7705297384379330eb39bdfd1b2/1241_8FW-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_8FW-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/121fba5be8172777ccb3b572f9e810/659_dCI-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dCI-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/5a3e1bb4920d1d28deec3511f1adbb/659_eqd-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_eqd-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/fe2cc688df734268796c756c04f1d7/1241_BJLE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BJLE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/f507ebe715b005684056c0b24bc5d8/1241_BSNP-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BSNP-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/66654cfc04d87aee844f8adfb567e3/1241_BOVC-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BOVC-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/3c5b7f19989c09eac223161a0ab287/1241_RON-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_RON-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/f15461d78c751da52d5479c0262141/659_dXQ-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dXQ-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/a1a3a59bc31fed2e5d44f217b5ae6e/1241_PJW-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_PJW-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/7aa4a723ca029f3a970dd3d3c475c9/659_eyD-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_eyD-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/713282ab15d1353560cdcca3b65281/659_ef5-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_ef5-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/80c7942047b58f0694942cf9285c2a/659_e5-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_e5-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/59433744f03dc3f617cf61247cd01a/1241_RY0-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_RY0-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/20ace587e446d8f67ef5a607387455/1241_B1B5-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_B1B5-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/1a82a6160f72d23a0d267f2356a39e/1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/d2ce00759067c47f9c88d44e14402f/1241_BLSX-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BLSX-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/5778dd01e49f22e6fd889b03676be9/1241_TAC-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_TAC-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/015c282d09797e4bbbe2aa7a1a928e/1241_BL2X-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BL2X-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/84cd0f5cbbd60d1e7ea1c531080814/1241_BKG2-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BKG2-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/2ddb40879585c696ddd69a2258160f/1241_Y4U-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_Y4U-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/703291eea99c56eb7f043e494aeda6/1241_33Y-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_33Y-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/36478e970a6752a34c5b9ae59d2ddf/659_bV0-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_bV0-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/57074a7d814357144d5e77d85ff922/1241_BQ0C-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BQ0C-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/263ebd2041ab886240358ad4814baa/1241_BQT4-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BQT4-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/c77a55fcb2b1f0b960b00ded2be024/1241_DG1-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_DG1-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/4841789e43b80f39fd349e13e1f18e/1241_BHR9-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BHR9-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/3e8e4331550c65350ea0416de90466/1241_KLI-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_KLI-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/8d3bea393585c7a71d9c75f762fc01/1241_NT4-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_NT4-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/e3bebd0feb323f1915c898aaeb3250/1241_JC4-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_JC4-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/efb61187cae5154839079325f933ab/1241_BVJC-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BVJC-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/0cb4b527fb6752f428f090a3cf85bc/659_doL-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_doL-N1-BDNA-1_A23TY32LT4_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/37/d25f57bdeb3c64fcd512afd7e51f21/1241_QPE-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_QPE-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/60e09a8f060378525f800c1d7b2bd3/659_dT3-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dT3-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/e56a6e2fd6c1b8879e13c5e2609809/1241_QW2-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_QW2-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/6f3ded0559517219f385e130044b13/659_dPb-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dPb-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/5c0cfac5249a7368101592c07c4ed7/659_cpY-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_cpY-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/511726c81f482224a064141186abf6/1241_BUK5-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BUK5-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/9119b5e4e4067a0049e5244c70b85f/1241_BQM9-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BQM9-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/383f0481cf7d976fd448c6aa923e84/659_bNj-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_bNj-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/c0f7bdda21b21d6bb746437e92e16d/1241_J22-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_J22-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/1af66e001ded9b8bd5041354c2b0c3/1241_SYH-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_SYH-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/41aa7ff8766be63885d66517dcb3a9/1241_MJG-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_MJG-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/dc6a2d0304586da5fb36944833d47c/1241_B2HF-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_B2HF-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/54bb3bbbf82dde5bd6f8d71861388b/NTC_0002_0036_A23TY32LT4_1_counts.tsv NTC_0002_0036_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/864bb48449f6c229e4e327057d5db3/1241_B3PP-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_B3PP-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/0001a0dbe3d088a7d1caa712b2784e/659_bST-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_bST-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/a4573b36503f514b612e12ac0e746a/1241_W16-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_W16-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/6ba7564c1b67db290b85263fb3de84/659_dB3-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dB3-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/b123aaf8179c8d43850ba9bc4a7139/1241_BC3K-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BC3K-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/0aea243ce6159cfb6fb87a9491f82b/1241_0R8-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_0R8-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/0b5f6438d464d73f0ce2db5968436d/659_cvt-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_cvt-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/189e141e7f5ffa853db9e8468ca84d/NA12878_c_0002_gDNA_0002_A23TY32LT4_1_counts.tsv NA12878_c_0002_gDNA_0002_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/83db39189046c6a9bb376e32d0b683/1241_BV1K-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BV1K-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/b8ef458150d702af59109c901cf24b/1241_ERK-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_ERK-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/1961780a80ebbc423adc4931bfb7a9/659_ekC-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_ekC-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/a7f5d68985c8f66d766f59f7ec6720/1241_BK2S-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BK2S-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/73256fec721e632478b9f6f8176815/1241_BT30-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BT30-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/b6aad65b3fb2cbaa9ce3b574ca53ee/NTC_0002_0027_A23TY32LT4_1_counts.tsv NTC_0002_0027_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/79cae7a2ef5b45121eb23184ebb5a9/1241_BTQN-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BTQN-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/7ff8d6b3fc979006d0a6ccf90065c5/1241_BHCY-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BHCY-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/e0f3f65b24773f0e85b233e65db534/1241_BWPR-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BWPR-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/aa01c4b6c304c9d4a2d690c566488c/1241_BAPK-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BAPK-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/083bf10d45926f4a1e874788ac2df0/1241_6R0-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_6R0-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/0d982093e8f9edf8de3eed98275601/1241_296-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_296-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/07937df5779f09f9f351b713b7616b/1241_QMS-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_QMS-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/fdd1636253cbbb99e9dd7d87823d9e/1241_BV6H-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BV6H-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/0ff4310945f742ef80d1d942ae4d7e/1241_FJT-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_FJT-N1-BDNA-1_A23TY32LT4_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/tmp/d9/e9adc47d523bdc17bcb280ea6e5672/germline_cnv_input.csv germline_cnv_input.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/58177b5040717e8657523b876ddcb0/1241_DTD-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_DTD-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/301f50992b31a2bd88ba8c9496ab60/1241_NXF-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_NXF-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/71b56982ea0b4e3e40fd5e6197c1e4/NTC_0002_0029_A23TY32LT4_1_counts.tsv NTC_0002_0029_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/fb657702a6d10b82372ce755ceb238/1241_B245-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_B245-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/781d62c622784d2e4de25439a6d0bd/1241_BXGB-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BXGB-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/f2682f0a7231beba20dd51d1ea6533/1241_FG3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_FG3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/4635891f93b2cb744e051e2bebd4c1/1241_BP9P-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BP9P-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/831636fcc6d94f7473d9e5ab013940/1241_URP-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_URP-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/0b19981bdd0692ae6fb68aed8bde6f/1241_BUM2-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BUM2-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/85b7ffd670e385fe35e2d8e0a48e0c/1241_Z5S-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_Z5S-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/1e2bb2900230ae810d361e8803e84a/659_dKV-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_dKV-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/e7c6e2415bf4d82cce5642209bca48/659_eOZ-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_eOZ-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/230a380a628b7af39b0762d009c2c7/1241_OUX-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_OUX-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/8b7e341a9366931ad7c64fefe5120a/659_e6H-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_e6H-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/9f97367cbf0b7037c024404adc7de8/1241_B215-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_B215-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/1e5b6afc453da6ce835d12f91f3ea1/1241_R33-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_R33-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/db1bf76397eb1eb8f16a727f73f023/1241_ULB-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_ULB-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/0a746e86025f9064ba90cac45dcde6/1241_BGI3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BGI3-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/c1317e4b087aa0287c1a01c9c4c10d/659_bl1-N1-BDNA-1_A23TY32LT4_1_counts.tsv 659_bl1-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/eff4480a547437824057e4f0add0c7/1241_E4B-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_E4B-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/302ed39af1241f64509c33a1692480/1241_BUKR-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_BUKR-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/25136680db71273ef40f3c1b682541/1241_BO6T-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BO6T-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/20ce9ed4d5e028fc0287a28f37eee1/NTC_0002_0038_A23TY32LT4_1_counts.tsv NTC_0002_0038_A23TY32LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/bef98abf6b6acc72eaf9638a592516/1241_3SE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_3SE-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/31b3f8af49e9f44e9af86892253ccc/1241_DW4-N1-BDNA-1_A23TNVNLT4_1_counts.tsv 1241_DW4-N1-BDNA-1_A23TNVNLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/a0348191edfd13fcb255105e9bcf83/1241_BV8U-N1-BDNA-1_A23TY32LT4_1_counts.tsv 1241_BV8U-N1-BDNA-1_A23TY32LT4_1_counts.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (197 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d counts_1.parquet sample_metrics_1.parquet ploidy_1.parquet B23KGCJLT4_1__sex_calls.parquet B23KGCJLT4_1__sex_calls.png" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/b84e098cdd503ac274dd4fbe4f1c44 || 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/3f/b84e098cdd503ac274dd4fbe4f1c44/.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