#!/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'
### - 'A23TY32LT4_1__sex_calls.parquet'
### - 'A23TY32LT4_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/b6/9133afffd640c1c36c35f2745858a5/.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/93/d150d0a64562aae428b952eab0a7b5/1136_7EX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_7EX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/fc2f85ed5aad62eed79a5bbc471af9/NA12878_c_0003_gDNA_0002_A23H3W5LT3_2_counts.tsv NA12878_c_0003_gDNA_0002_A23H3W5LT3_2_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/a47891febd0da8a0129eb0d200e8b8/1029_BPC3-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BPC3-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/fa5d21a609b57c52dd45cac5eb51a8/1136_22N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_22N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/c568abddc453afbf89d6fae94019f4/1029_CWN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_CWN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/9e705abe70d39fa6053c3d4f926e49/1136_1V8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_1V8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/e9ba96c9282ba64f806477c2f8e9fc/1029_1UX-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_1UX-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/234ee6162b13f588ed9c218d005def/NA12878_c_0002_gDNA_0002_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0002_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/c1da56348ab6285874cb0b8c107f28/1029_UCZ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_UCZ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/4a46528c71c87274ed2b6956dd7fcb/1136_251-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_251-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/c1c1370646a78cab153ae904a32d38/HG00259_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG00259_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/142d688693a82fdd974f97d6b18e96/1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/d2496275921662a1ccfe948739a985/1136_23E-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_23E-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/110710a29e8153ec76497e9633249a/NTC_0001_0001_A23H3W5LT3_1_counts.tsv NTC_0001_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/b8bcaac16117acd5a70ffe854502b1/1173_PCB-N1-BDNA-02_A23MHW3LT4_1_counts.tsv 1173_PCB-N1-BDNA-02_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/f2a11f7a52fe6acaa6294369553831/NA14234_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA14234_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/9ae811992d9516fcfd619f7b40e8c4/NA07106_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA07106_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/a85d2314c7aacbf9900fdedeabb7a0/1136_29V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_29V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/33d252a1aa129ac355ccf932692f07/1029_W7S-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_W7S-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/9163e8412e79c8854e344ddea455be/1029_B1C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_B1C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/8f465639e9a0df7bd0b95c62a4f537/1136_4HJ-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4HJ-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/25748556cb1e262bf4d63e0d99f51b/1029_MB8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_MB8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/a90088daf5f09d23ee85bfa520d0dc/1173_J3R-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_J3R-N1-BDNA-01_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/78fefca09182410e524b44815d34e0/1029_NXR-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_NXR-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/3dc0c0d206711568f507ae117abadc/1029_BTW1-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BTW1-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/059f638b9384d0ede595252576fa66/1029_JJU-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_JJU-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/634ba269f0fd5419a7c576c03ff2d6/1136_2DN-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2DN-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/55d35ab3e06bf6a36a30bf2667593f/1173_NWE-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_NWE-N1-BDNA-01_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/e7456aefa7f02f9aa516fbca474fa4/NA07891_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA07891_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/51615c3791a9730807f737e11a9f40/1029_MH0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_MH0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/45ac90283ea86d3fd91fd47790b9c5/NA13451_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA13451_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/8f4cca71f3ab401c92d7d685b97344/1136_84H-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_84H-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/2229b6aebfe499fa61396ddf29eca9/1136_13-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_13-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/44f8ac1fc66caf48796e1dd650f145/1136_0B-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_0B-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/7666c7c3fe9da5ae060820aefacdc0/1029_ROB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_ROB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/590147c889edbbefc8fffa6f294625/1136_20N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_20N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/4e457223f4735773f1bdb78df38c64/1136_10H-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_10H-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/a811d6a79ff81e1c45c0426f9b9cba/1029_BF1C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BF1C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/475ef8ec02dcb90a4236876734af49/1136_02S-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_02S-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/bd33e106a3380345e201268b0dfe7a/1136_2HR-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2HR-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/319a3c4d1a316278689f7a2cc57df0/1029_NMM-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_NMM-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/15612137c036a8163064b173e94ffe/NA03184_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA03184_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/5e5cbb7182a8902600f66268466294/NA12878_c_0002_gDNA_0007_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0007_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/d2ec28f9f835d8e7006c188e1e0393/1136_8EX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_8EX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/ce973b5fc62f1f5242665e5ed9136f/NA14626_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA14626_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/0f386e7f20b5a7a7d70f8eed8b0f73/NA19404_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA19404_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/ba09bf1d9dfc3f00c8f1a8332e1f16/NA08618_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA08618_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/0a5093d26a8b0221685aafa34c5b75/1136_5FD-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_5FD-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/0a28a06ef139c8ca8a912d4466a804/1029_BNMN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BNMN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/f2deb72066f426c6ee59d43b7570c1/1029_D19-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_D19-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0194ce9c277496dafb8a42fa8d773f/1029_NHT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_NHT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/25d475fe655c4ba3b8f79458954091/1029_BCTD-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BCTD-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/95c6f370fe5b5ec385e3a579714ac9/NTC_0002_0002_A23MHW3LT4_1_counts.tsv NTC_0002_0002_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/859e53065c81cc16a672364a7e82a4/NTC_0001_0001_B23H2GYLT3_1_counts.tsv NTC_0001_0001_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/b3137424b38ca02a7bf1161e2f136b/HG00731_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG00731_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/eba15f064e9688c0a97d4be1bebf33/HG02977_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02977_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/0d3923a7e73db24dd8ecfcc819591e/1136_25Q-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_25Q-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/0d5ec5be31fa76fd6abd81febde69e/1136_0JP-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0JP-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/bef0a3681a65127282028fb4271983/1029_C3S-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_C3S-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/a5d9d0a88fda210033ade8f173fe31/1136_3T8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_3T8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/75f52612cc4525d6444ad1d48ef38d/1136_2AR-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2AR-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/2d13adb040308a73ed974959bbe401/HG02111_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02111_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/b093d46c2fefa99be2ea7ab9d021ee/1029_WTT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_WTT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/607b774c0d6fd93431788e586c0656/1136_2FY-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2FY-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/8c1ebcdf2032caf87788d85b1fe48b/1029_BQ3K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BQ3K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/4cede0ddf6a8161e550a8993028479/1029_RCF-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_RCF-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/dc74c47240100794d248139c8d990d/NTC_0002_0001_A23MHW3LT4_2_counts.tsv NTC_0002_0001_A23MHW3LT4_2_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/29974e54d47686c346eef102fecfa0/1029_GP0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GP0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/1c8553c5d7f2b6574075d63d8e651b/1136_2B2-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2B2-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/379f0079e373884eeb379271ebcc8b/1029_W1O-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_W1O-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/fd2e502f538b81b8c7c3cd49a1890a/1136_0T4-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0T4-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1cd86a77b529ab1471f49ca04a5a55/1136_2GE-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2GE-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/8e7747fd58ee1783ab8523f2904995/1029_V13-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_V13-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/04e32138ddb9dc0400b804dfcfdd13/1136_024-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_024-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/1a7a529fe0ec0eadd778b88ea96bf9/NA12878_c_0003_gDNA_0002_B23H2GYLT3_1_counts.tsv NA12878_c_0003_gDNA_0002_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/98053e73a466a1a279080e406626ed/1173_9C-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_9C-N1-BDNA-01_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/97167fc992706818b961910395436b/NA01359_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA01359_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/ae63419c934e18d5fcd8d890512446/HG02878_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02878_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/9a023610d9b0a59904d52ee49f9d94/1029_P0W-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_P0W-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c1dd254550d49e3983a723183e7551/1136_47X-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_47X-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/182634dc0d014466f05da1ecf8fb14/1136_1UN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_1UN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/308062902060409de38fb200cb74d2/1136_4VV-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4VV-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/89b2ce3ff11d43bd132530f40c6284/1136_0UA-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0UA-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/a488777e3037aebd4d1481502952ab/1029_OHN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_OHN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/761457bf994d37ecfa1355c46dcaa4/HG01242_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG01242_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/13f08ea7ef89dd24948097549a7b55/NA01535_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA01535_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/9ef51958acc4fbd2287b987d7aa458/NTC_0001_0001_A23H3W5LT3_2_counts.tsv NTC_0001_0001_A23H3W5LT3_2_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/671fbd3316a5065c3b78bc70e36e56/NTC_0002_0047_A23MHW3LT4_1_counts.tsv NTC_0002_0047_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1e053eb77f97345bde4417356d4f74/1136_229-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_229-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/a3d7f65d35135fd3a6918d644ccf52/1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/42f5cc9aecb8ec80933d4df226fa8c/1136_0NH-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0NH-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/5deb35a3d468b89293e336ebc7a17f/1029_BI3C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BI3C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/e1d8e2409cc2156a76daf21ab90c49/1029_GWX-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GWX-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/21b7dc368745ffff38a4e18e318a01/1173_CRL-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_CRL-N1-BDNA-01_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/ccb6b68a77770528381991af01874d/1136_03N-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_03N-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/d7d330f730996d46da13ee8be49fe1/1136_4HC-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4HC-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/01c7e52f2b1d2743383e7f98d3f615/1136_8FN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_8FN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/3736f94d06347a0c5f76b1e2660663/HG03259_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03259_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/8bbbe6fce8af87a34cfd15a1067201/1136_4SO-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4SO-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/32768de4cf2c5478e0b92c46f07724/1136_5W-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_5W-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/c2f6d087d641b1129c94e1d2ef9c53/1136_5CN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_5CN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/d7ec175efeda6c16d89e66d95c1fc5/1029_LNB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_LNB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/6be8b935ef403168f67ac8c68a78ba/1029_GNJ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GNJ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/0dd2b75abfe75dc62185c62f3ce300/1136_0PG-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0PG-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/edb6aabad4a1c78d4bdf0e2d0e0d40/1029_Q3K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_Q3K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/bfcedcb301f646c46c4e609a9699d2/1136_24I-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_24I-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/0c9b0d6214b037a95cb6823573bc98/1029_3PB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_3PB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/92e905fc381b95cd968222ae0ea941/1029_7OE-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_7OE-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/13af81911d0dc689a5aad5ebdf3a98/1029_22Q-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_22Q-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/af1fcae551d1a5798bdc7b39a4cd0b/1029_BLVT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BLVT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/f874a0346056667e936ae3de6f4382/1136_24Z-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_24Z-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/53a5a5a1dcbdd7c18e590e704f49d4/1136_7F8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_7F8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/59bbb4344f7dde7e1631bd09106d51/1029_DQI-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_DQI-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/5a757cd20f54aa8207cad11bdc9e7e/1029_BL7I-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BL7I-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/5e2064c55a75c003c487bdabf547d9/1136_2CZ-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2CZ-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/381e001bb6331ea7fa96d47d8bea27/1029_26C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_26C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/83d673d12eed67909b5300be887df6/1029_UKQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_UKQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/acd7c8174d9a6e460f8d2cf843ccfc/1136_2C0-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2C0-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/6c3143e5e0f22d3beb910d4212c4ca/1029_KR2-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_KR2-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/be45b5024657f4093d6a5ffcf20791/1136_2HX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_2HX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/d42b636434b6a469c3f190d644a8d3/1029_GG5-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GG5-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/2aa9c48fe925e2ee853b1c7bbcb607/1029_BMDN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BMDN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/3f5badf49167a9eada6ee108f22deb/1029_BGPR-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BGPR-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/504b8b00f13f3c443e6693c0529dc4/1029_BNM7-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BNM7-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/1f2765cd54697c0743b877687731ae/1029_1EQ-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_1EQ-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/c67cfb11243ebbc8c504c0b976466d/1029_BKJD-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BKJD-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/928c9ec8f2140a6d50adab4d7314b0/HG03857_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03857_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/5183f81428b6cebbe92f7409d94e9d/NA12878_c_0002_gDNA_0008_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0008_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/0d67e414549019327d0ae13da79266/1029_BON7-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_BON7-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/4116edb8336c55dfebb51968ab35cf/1136_4DY-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4DY-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/143902b156acac3cceaa24ecaf8c9f/NA12878_c_0002_gDNA_0001_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0001_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/5f5f78e2630c35668c30ae7ee4f673/1029_BQ0K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BQ0K-N1-BDNA-1_B23H2GYLT3_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/71/218e3ddd45d592650b05817cdcb810/1136_26U-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_26U-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/6ce1a0840667bd344b7be8f9300b0c/NA11570_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA11570_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/88d9cc720b51d008bc950d54739cd4/HG03694_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03694_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/1ff9b1891992b4d2dc1602cba01458/HG02982_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02982_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/c32227622541d38e4e5e46c0c954b7/NA12074_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA12074_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/848bc6b050ea3dbca8a349624a7dfe/1136_2FO-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2FO-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/e22cea632ccb91ac659d17d18e05f9/1029_344-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_344-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/048731766fe60a7870cc136f73d689/1136_2BI-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2BI-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/0299690a31062647b7a20822723992/1136_0EH-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0EH-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/20f28fdccde610faf5191a03f0f456/1136_282-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_282-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/d53c1748e0cf992d3a568bd0d4a752/1136_3K7-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_3K7-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/812a7aa55b253afba8b8a4c57ee1de/1029_G7F-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_G7F-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/7940999fde99c4ba5f854fe90c2d50/1136_250-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_250-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/2777ec6b03e6aeb35ff5f3564c2615/1136_200-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_200-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/6f53164fce51d56b649c0bd50b203a/1029_M9U-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_M9U-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/acebd1a0045bbde5a78f735c370fd8/NA20539_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA20539_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/3c025e53f211371f86fbd9b566b412/1029_1CZ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_1CZ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/314aa2af212ec64a15f058e3af27c3/1029_XPW-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_XPW-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/e048180f989ead233d4e74bbd525b5/1029_BOCP-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BOCP-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/7d24ef44c2cd30ebadb2c334a01e3c/NA12606_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA12606_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/b9b8d6dea95b10f18faee5d0553fa3/1029_4X0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_4X0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/6f65a3ba264b70c0ffeeb4caba5f29/1029_BBPA-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BBPA-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/7b21e14b3687fae03108ddb4d5c237/1136_35Z-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_35Z-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/4d00ad85e5d6099f4b1c7a624c4401/1136_211-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_211-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/8e7de5b7ba17eaca0affda9a13ad69/1136_26N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_26N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/f9306ce527e3201962e7db18db4513/1029_KET-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_KET-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/78d752c88a06bcc05ed3dddd1b1f35/HG00187_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG00187_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/cd65bd11b07124f07d6c68e7153798/1136_04F-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_04F-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/8549a59d68d6b9a1db77d59b746ce5/NA03226_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA03226_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/f3fb762dd312b2d1821a4c2a4b1b6a/1136_0YQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_0YQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/0d6dbf666c8c8f910ac50b44ff5c28/1029_YHI-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_YHI-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/123b696cbcca0f35d6d1f4512a6b0e/1136_0W-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0W-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/5c728dfc2677131b37b02497e97447/NA12878_c_0003_gDNA_0002_A23H3W5LT3_1_counts.tsv NA12878_c_0003_gDNA_0002_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/68d0f8c55b9bdabe644eedf3c65881/1029_7AL-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_7AL-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/4223eaa76ef43ab5b879e81cbaea36/1136_2FA-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2FA-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/0745e8249bdd1c3c2a3dec113e8c89/1136_25V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_25V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/2422c3ef5c9508916cdbec16376b9d/1029_BNY-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BNY-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/d5574b7b0b023cafa237071bb667ef/1029_BDK5-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BDK5-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/a29ad1527e40018b5cda4ded1589cf/1029_I2Q-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_I2Q-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/7f857e9737b29a25785b1c719ea696/1136_209-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_209-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/a669eb5fc5231601555bec25d347ce/1173_NMN-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_NMN-N1-BDNA-01_A23MHW3LT4_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/4f/20b7ddc9e9ed41d760bb04d214ba23/germline_cnv_input.csv germline_cnv_input.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/483685d2b1d72e16165e9ab9bbb10c/1029_BO4N-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_BO4N-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/02c4ea9aa28efe9ed80a2d8ae98ff6/1136_19H-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_19H-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/a460041c19eaac2b67842c5581c678/1136_7FA-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_7FA-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/fced863a5977137d074e1ba1f74ac5/1029_DB2-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_DB2-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/8474bd1df66feb9206d7aa98172ce5/1136_203-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_203-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/a42cf3f62481e4142c3573023182ea/1136_67V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_67V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/3f2c611830869c2dc0ffcb55ade340/HG00634_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG00634_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/881d2713b8932a5905481da968c054/1136_20M-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_20M-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/a17a45ee86d32f277947a243c8ed40/1136_25E-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_25E-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/cc837f98d45e907b087f72e58aefd9/1029_R8U-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_R8U-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/0a31f49dd5b2c89a25d49a06a831bb/NTC_0002_0001_A23MHW3LT4_1_counts.tsv NTC_0002_0001_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/3229ff28ebba78e88000e2f291082f/NA07081_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA07081_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/e8cb83470eb775fd7bfa7ecc168293/1029_BC9J-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BC9J-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/add3ce5b82234967becfb89cb81c58/1136_6C2-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_6C2-N1-BDNA-1_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/0d4049d6e11f527d29d5c62a87d320/1136_2GM-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2GM-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/ecf930d2926d63ed0a091796844991/HG03267_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03267_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/35c2f2ec9cfa2da5dc4b14d2dc8695/1173_JLC-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_JLC-N1-BDNA-01_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/a321e07543b0ef5c3490c56b6009d1/1136_20J-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_20J-N1-BDNA-1_A23MHW3LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/a109c1c43b9b04796e4eff289d8938/1029_3HC-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_3HC-N1-BDNA-1_B23H2GYLT3_1_counts.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (197 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d counts_1.parquet sample_metrics_1.parquet ploidy_1.parquet A23TY32LT4_1__sex_calls.parquet A23TY32LT4_1__sex_calls.png" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/9133afffd640c1c36c35f2745858a5 || 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/b6/9133afffd640c1c36c35f2745858a5/.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