#!/bin/bash
### ---
### name: 'SOMATIC_CNV_REF_BUILDER:SOMA_CNV_BUILD_REFERENCE (build_reference)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-3cb5ec5'
### outputs:
### - 'batch_reference.parquet'
### - 'sex_calls.csv'
### - 'feature_stats.csv'
### - 'versions.yml'
### ...
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}

nxf_tree() {
    local pid=$1

    declare -a ALL_CHILDREN
    while read P PP;do
        ALL_CHILDREN[$PP]+=" $P"
    done < <(ps -e -o pid= -o ppid=)

    pstat() {
        local x_pid=$1
        local STATUS=$(2> /dev/null < /proc/$1/status grep -E 'Vm|ctxt')

        if [ $? = 0 ]; then
        local  x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
        local  x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
        local x_peak=$(echo "$STATUS" | grep -E 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
        local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
        local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
        local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
        cpu_stat[x_pid]="$x_pid $x_pmem $x_vsz $x_rss $x_peak $vol_ctxt $inv_ctxt"
        fi
    }

    pwalk() {
        pstat $1
        for i in ${ALL_CHILDREN[$1]:=}; do pwalk $i; done
    }

    pwalk $1
}

nxf_stat() {
    cpu_stat=()
    nxf_tree $1

    declare -a sum=(0 0 0 0 0 0 0 0)
    local pid
    local i
    for pid in "${!cpu_stat[@]}"; do
        local row=(${cpu_stat[pid]})
        [ $NXF_DEBUG = 1 ] && echo "++ stat mem=${row[*]}"
        for i in "${!row[@]}"; do
        if [ $i != 0 ]; then
            sum[i]=$((sum[i]+row[i]))
        fi
        done
    done

    [ $NXF_DEBUG = 1 ] && echo -e "++ stat SUM=${sum[*]}"

    for i in {1..7}; do
        if [ ${sum[i]} -lt ${cpu_peak[i]} ]; then
            sum[i]=${cpu_peak[i]}
        else
            cpu_peak[i]=${sum[i]}
        fi
    done

    [ $NXF_DEBUG = 1 ] && echo -e "++ stat PEAK=${sum[*]}\n"
    nxf_stat_ret=(${sum[*]})
}

nxf_mem_watch() {
    set -o pipefail
    local pid=$1
    local trace_file=.command.trace
    local count=0;
    declare -a cpu_stat=(0 0 0 0 0 0 0 0)
    declare -a cpu_peak=(0 0 0 0 0 0 0 0)
    local mem_tot=$(< /proc/meminfo grep MemTotal | awk '{print $2}')
    local timeout
    local DONE
    local STOP=''

    [ $NXF_DEBUG = 1 ] && nxf_sleep 0.2 && ps fx

    while true; do
        nxf_stat $pid
        if [ $count -lt 10 ]; then timeout=1;
        elif [ $count -lt 120 ]; then timeout=5;
        else timeout=30;
        fi
        read -t $timeout -r DONE || true
        [[ $DONE ]] && break
        if [ ! -e /proc/$pid ]; then
            [ ! $STOP ] && STOP=$(nxf_date)
            [ $(($(nxf_date)-STOP)) -gt 10000 ] && break
        fi
        count=$((count+1))
    done

    printf "%s\n" \
        "%mem=${nxf_stat_ret[1]}" \
        "vmem=${nxf_stat_ret[2]}" \
        "rss=${nxf_stat_ret[3]}" \
        "peak_vmem=${nxf_stat_ret[4]}" \
        "peak_rss=${nxf_stat_ret[5]}" \
        "vol_ctxt=${nxf_stat_ret[6]}" \
        "inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
}

nxf_write_trace() {
    printf "%s\n" \
        "nextflow.trace/v2" \
        "realtime=$wall_time" \
        "%cpu=$ucpu" \
        "cpu_model=$cpu_model" \
        "rchar=${io_stat1[0]}" \
        "wchar=${io_stat1[1]}" \
        "syscr=${io_stat1[2]}" \
        "syscw=${io_stat1[3]}" \
        "read_bytes=${io_stat1[4]}" \
        "write_bytes=${io_stat1[5]}" >| "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
}

nxf_trace_mac() {
    local start_millis=$(nxf_date)

    /bin/bash -Ceuo pipefail .command.sh

    local end_millis=$(nxf_date)
    local wall_time=$((end_millis-start_millis))
    local ucpu=''
    local cpu_model=''
    local io_stat1=('' '' '' '' '' '')
    nxf_write_trace
}

nxf_fd() {
    local FD=11
    while [ -e /proc/$$/fd/$FD ]; do FD=$((FD+1)); done
    echo $FD
}

nxf_trace_linux() {
    local pid=$$
    command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; }
    local num_cpus=$(< /proc/cpuinfo grep '^processor' -c)
    local cpu_model=$(< /proc/cpuinfo grep '^model name' | head -n 1 | awk 'BEGIN{FS="\t: "} { print $2 }')
    local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
    local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
    local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
    local start_millis=$(nxf_date)
    trap 'kill $mem_proc' ERR
    
    /bin/bash -Ceuo pipefail .command.sh &
    local task=$!

    mem_fd=$(nxf_fd)
    eval "exec $mem_fd> >(nxf_mem_watch $task)"
    local mem_proc=$!

    wait $task

    local end_millis=$(nxf_date)
    local tot_time1=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
    local cpu_time1=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
    local ucpu=$(awk -v p1=$cpu_time1 -v p0=$cpu_time0 -v t1=$tot_time1 -v t0=$tot_time0 -v n=$num_cpus 'BEGIN { pct=(p1-p0)/(t1-t0)*100*n; printf("%.0f", pct>0 ? pct : 0) }' )

    local io_stat1=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
    local i
    for i in {0..5}; do
        io_stat1[i]=$((io_stat1[i]-io_stat0[i]))
    done

    local wall_time=$((end_millis-start_millis))
    [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"

    printf "%s\n" \
        "nextflow.trace/v2" \
        "realtime=$wall_time" \
        "%cpu=$ucpu" \
        "cpu_model=$cpu_model" \
        "rchar=${io_stat1[0]}" \
        "wchar=${io_stat1[1]}" \
        "syscr=${io_stat1[2]}" \
        "syscw=${io_stat1[3]}" \
        "read_bytes=${io_stat1[4]}" \
        "write_bytes=${io_stat1[5]}" >| "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"

    [ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true
    wait $mem_proc 2>/dev/null || true
    while [ -e /proc/$mem_proc ]; do nxf_sleep 0.1; done
}

nxf_trace() {
    local trace_file=.command.trace
    touch $trace_file
    if [[ $(uname) = Darwin ]]; then
        nxf_trace_mac
    else
        nxf_trace_linux
    fi
}
# bash helper functions
nxf_cp_retry() {
    local max_attempts=1
    local timeout=10
    local attempt=0
    local exitCode=0
    while (( $attempt < $max_attempts ))
    do
      if "$@"
        then
          return 0
      else
        exitCode=$?
      fi
      if [[ $exitCode == 0 ]]
      then
        break
      fi
      nxf_sleep $timeout
      attempt=$(( attempt + 1 ))
      timeout=$(( timeout * 2 ))
    done
}

nxf_parallel() {
    IFS=$'\n'
    local cmd=("$@")
    local cpus=$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
    local max=$(if (( cpus>4 )); then echo 4; else echo $cpus; fi)
    local i=0
    local pid=()
    (
    set +u
    while ((i<${#cmd[@]})); do
        local copy=()
        for x in "${pid[@]}"; do
          # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
          # see https://github.com/nextflow-io/nextflow/pull/4050
          [[ -e /proc/$x ]] && copy+=($x) || wait $x
        done
        pid=("${copy[@]}")

        if ((${#pid[@]}>=$max)); then
          nxf_sleep 0.2
        else
          eval "${cmd[$i]}" &
          pid+=($!)
          ((i+=1))
        fi
    done
    for p in "${pid[@]}"; do
        wait $p
    done
    )
    unset IFS
}

# aws helper for s5cmd
nxf_s3_upload() {
    local name=$1
    local s3path=$2
    if [[ "$name" == - ]]; then
      local tmp=$(nxf_mktemp)
      cp /dev/stdin $tmp/$name
      /opt/s5cmd/bin/s5cmd --log error cp --storage-class STANDARD $tmp/$name "$s3path"
    elif [[ -d "$name" ]]; then
      /opt/s5cmd/bin/s5cmd --log error cp --storage-class STANDARD "$name/" "$s3path/$name/"
    else
      /opt/s5cmd/bin/s5cmd --log error cp --storage-class STANDARD "$name" "$s3path/$name"
    fi
}

nxf_s3_download() {
    local source=$1
    local target=$2
    echo "  Downloading: $source"
    local file_name=$(basename $1)
    local is_dir=$(/opt/s5cmd/bin/s5cmd ls $source | grep -F "DIR  ${file_name}/" -c)
    if [[ $is_dir == 1 ]]; then
        /opt/s5cmd/bin/s5cmd --log error cp "$source/*" "$target"
    else
        /opt/s5cmd/bin/s5cmd --log error cp "$source" "$target"
    fi
}

nxf_sleep() {
  sleep $1 2>/dev/null || sleep 1;
}

nxf_date() {
    local ts=$(date +%s%3N);
    if [[ ${#ts} == 10 ]]; then echo ${ts}000
    elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
    elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
    elif [[ ${#ts} == 13 ]]; then echo $ts
    else echo "Unexpected timestamp value: $ts"; exit 1
    fi
}

nxf_env() {
    echo '============= task environment ============='
    env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
    echo '============= task output =================='
}

nxf_kill() {
    declare -a children
    while read P PP;do
        children[$PP]+=" $P"
    done < <(ps -e -o pid= -o ppid=)

    kill_all() {
        [[ $1 != $$ ]] && kill $1 2>/dev/null || true
        for i in ${children[$1]:=}; do kill_all $i; done
    }

    kill_all $1
}

nxf_mktemp() {
    local base=${1:-/tmp}
    mkdir -p "$base"
    if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
    else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
    fi
}

nxf_fs_copy() {
  local source=$1
  local target=$2
  local basedir=$(dirname $1)
  mkdir -p $target/$basedir
  cp -fRL $source $target/$basedir
}

nxf_fs_move() {
  local source=$1
  local target=$2
  local basedir=$(dirname $1)
  mkdir -p $target/$basedir
  mv -f $source $target/$basedir
}

nxf_fs_rsync() {
  rsync -rRl $1 $2
}

nxf_fs_rclone() {
  rclone copyto $1 $2/$1
}

nxf_fs_fcp() {
  fcp $1 $2/$1
}

on_exit() {
    local last_err=$?
    local exit_status=${nxf_main_ret:=0}
    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
    printf -- $exit_status | nxf_s3_upload - s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a/.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/56/06fffdd98c711e2faedb5e0951c2f0/1029_URF-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_URF-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/621434bf6cdb78b868ba9792297669/1136_8DH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_8DH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/91a81da32e7652b5b26f17232234cf/1029_UY6-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_UY6-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/6c0b5572bae9bb7f425ce5db58833e/1029_TWA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_TWA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/3f4d058d110f758c7a7a1195c73cf0/1136_7SR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7SR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/d028adf1f9f3c2396d30d4f6719970/1136_6ZR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_6ZR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/fe608f454974ad975a4fac9f87e4d0/1136_46W-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_46W-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/cf8c68085a8fe76ef4db27055c9fd1/1029_H5W-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_H5W-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/4a600ca3c8abed195644c58be40135/1047_MI-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_MI-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/d1c5842cde839e1a47db43aba1e6a8/659_dhS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_dhS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/90f2727bab111ee347df2eef575b13/1136_6I8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_6I8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/985825eded68318ace2b8e08712d4e/1047_KD-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_KD-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/6daacade4ce92e4b15af875537f70a/659_3g-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_3g-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/c93b469e4e5e89262bebd99b902f6b/1029_BF8C-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BF8C-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/e83314274f6a6082b0513d52e8813a/1173_LAF-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz 1173_LAF-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/81c05a7988b189e554adee1f5b4a95/1136_7RV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7RV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/9a5f421e210594db61e401832683e8/1029_1O-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_1O-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/a785c391bf41de168dcaafeffcc3de/1136_881-N2-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_881-N2-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/386cd02d936a61df1450d1f6b9d47a/659_uv-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_uv-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/b704dabaa83f2624fa750c1fbcba66/1136_28T-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_28T-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/47c77d0e3650422aa38588a2404ede/1029_MNZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_MNZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/5fbb319b54ca9ee173add2706912e0/1029_J1R-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_J1R-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f390970a752cd2ee39429646b3f87b/1136_4SB-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4SB-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/25ea9f09e1c7fce30d8083af857a1f/1029_OIL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_OIL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/64ed71575a8b5e2967a285a67bd484/1136_2FR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_2FR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/b128046fa985ed15f01b9c355f9c85/1047_K3-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_K3-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/07078764bf8f08290625c429f4d62c/1029_H34-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_H34-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/1ed80be0144ce97aa60f7319ee4e7d/1029_BJUI-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BJUI-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/e73dd3dc62d3c53c0026b7c9d8f7c2/1047_M8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_M8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/a1ce8ea6b387aed45288b65bc61bdf/1029_HS0-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_HS0-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/a7db32f1f665cf4c860ea321d0477b/1136_2JR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_2JR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/6ee47c1601dca6f481cf2d414dbc7d/1029_BD47-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BD47-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d7dea94f8cb5983fc0495da496933b/1136_00K-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_00K-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/9867a760193b04e479a5c2ebe38648/1047_L2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_L2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/75e969ec586e61d968739c5564c1ed/1029_JH5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_JH5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/08e4c9012defbe8a908064451b24ab/1136_44E-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_44E-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/b34a774619b9e31110954845327c34/1029_92F-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_92F-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/309946bd75ee0d5f070bf759c04f40/1047_K7-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_K7-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/92a907f4b4a621079915de3229f2b9/1029_627-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_627-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/ff7d322c671b95aeafa2293de5ce23/1029_LMJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_LMJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/af52db7c418c70fe9faef25ff417fb/1047_LM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_LM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/89c4a140ef22b714c0c792a88c0be2/1047_N1-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_N1-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/c1319609f21165c82b75be1a96ecdb/1136_682-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_682-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/9f457496edb3e81de2da49c2998f24/1029_IYM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_IYM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/84be97759013987ffe051e708f7067/659_cst-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_cst-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/e6ec28c6229cb1f8a8fc5e2885c822/1136_54L-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_54L-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/9adc42fb2dbefacc03ad309105e386/1047_K6-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_K6-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/7dba52e8c0500aa3e34a5723c55bca/1029_WTV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_WTV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/5bc9f76543153f7fb8af5ceef42a5f/1136_862-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_862-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/3712d941aa7c2c0394dbe0f5d2af56/1029_KOC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_KOC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/625963c513f84b6748574c44f4d632/659_b6q-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_b6q-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/6ba59bff303728d6af99be3b0d1e28/1029_MUC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_MUC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/e3b34760affc48a414a4a639cfa61f/1173_GZ1-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz 1173_GZ1-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/66d800aa93e0963b0dd71f0a2ef341/1029_PDM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_PDM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/874019346e4703ca2e6fca6d7d38ee/1136_7B-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7B-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/642b644725df93a4e66a25aed102e6/1029_ZFT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_ZFT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/9bc9e51941a053483ff10381df540e/1136_3BF-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3BF-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/2bfbc8188e486150e6fde6e2bdf7e6/1047_OH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_OH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/3451b6ca964891174862f480540df0/1136_7ZM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7ZM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/3fda04876b748c9d426c98adba67ac/659_Em-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_Em-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/edb3600173577be6ac63ee21b4dbed/1029_IVL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_IVL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/1b379e078b0f3fec601824934a974b/1047_OO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_OO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/ce16a70392cc685f633447018cebfc/1029_NIG-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_NIG-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/7edf90c4aee946c9adce654904bee3/1173_F0Y-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz 1173_F0Y-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/2e8536e72a49bc2a835c9f1b447118/1029_EI7-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_EI7-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/7eb7e9186755865b4d5c9e50af88b6/1047_JZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_JZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/d45d84878b5da2c838ba0267c62522/659_Jq-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_Jq-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/8d4c4a4665ab42fab9de6791ed0b57/1047_MT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_MT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/81a4770a5afd5972edfc622f7bd1ed/1029_LXR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_LXR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/bfecb2cfa5a8eee737ab8b555da91b/1047_NK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_NK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a/.command.sh .command.sh")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/a1126ac3409e786d73b31aa0f813ed/1029_SX3-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_SX3-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/20be98097b77b7911c56d8b72518aa/1029_I4S-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_I4S-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/89517b196ab04e34592e0321ffcf15/1136_4OA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4OA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/112c8a3b4014c8787f5eda82d2e8fd/659_cIW-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_cIW-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/f4690949d76c6c31216b28f4e7668a/1047_ME-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_ME-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8d420e782c0efd1edce1d88fc65aaf/1029_KVO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_KVO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/19461b6cac14fb7141c3b5e903a5d7/1047_OJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_OJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/cedb99658ce8d298eb87117cd1a647/1047_LS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_LS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/535db87e72783173fa6cf29cb0284d/1136_73N-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_73N-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/9e45cb1325912a61af9c628b5fbfcd/1136_8D1-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_8D1-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/8adc931cc19de8ecc3526af7e7eca3/1029_FQY-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_FQY-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/c7e51fd9f5abb2ace2625691eaaafc/1029_JAD-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_JAD-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/f2c6c3711302e0fba59715c3dabe60/1047_O-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_O-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/9c33c8e64893b736afb64206ebf072/1029_S6H-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_S6H-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/b8afff7111a6d0339b2feb282f026c/1136_7JJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7JJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/7bcf069470656e1ba244324b651e1d/1029_KUX-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_KUX-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/44680b5d952ef6a5c676e4354c4916/1029_TMD-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_TMD-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/bbbae6300b44f70cd57f275eceb32f/659_d13-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_d13-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/53a5dfe579e621ce83d56cd5641af7/1029_H3N-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_H3N-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/64a401e030f47a4d8c19a462b7db38/1136_3Q5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3Q5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/cb01d3941af82e43c33bc7240d656a/1029_500-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_500-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/d7c54928554ae19386d7ef0c5d189b/1136_4JL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4JL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/394edfd230f8735b214cd391a1af73/1029_I5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_I5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/a847f56901e4a126e09168869da431/1047_KK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_KK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/b71f7314d74469b3e9f0089788bff1/1029_GI6-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_GI6-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/77c45ad691914a2ec31c4461fa2258/1136_67L-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_67L-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/f76ce5e6618c97f685c160ad8545f2/1047_OM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_OM-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/2a4eff555683072dda19a6a4f949e5/659_c53-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_c53-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/0ca4c88054427f30b683c8bbb12a6a/1029_LPB-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_LPB-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/bcd3dcaf36acebe8001103d8b59bc3/1029_RJ7-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_RJ7-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/5c4e7f9694c152d75d26f4cdb87e8d/1136_851-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_851-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/c8aa7c693ff21b2c3e9ed958e4bcff/1029_BQ8B-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BQ8B-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/fdff971f8ac4890d1a4cb786c43e52/659_bwh-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_bwh-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/16ed1057da4d3af3a4fef7cbabb7b5/1047_NH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_NH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/686a86319f0ae7955d52a2d8b8e637/1173_H2E-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz 1173_H2E-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/b5a8d2f2570e758c1b8292fd7055db/1136_3NL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3NL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/0507d76df28251d712af68463a65e2/1136_7V3-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7V3-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/5c1bef8f3544c3a61f5b2dbb259c3a/1136_2QX-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_2QX-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/77ed67e39d5c1af69d25f1d85bb9a9/659_dLs-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_dLs-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/ba35c8bdad4447f050001b62bac7db/1136_6V9-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_6V9-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/c96a0a5879c7b473ee6f7756e6c7ba/659_e6r-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_e6r-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/4116873a139a691f969c0bac5ab2e5/1136_4GN-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4GN-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/57d66a1a81e87477b2add9c9f4c6b1/1029_U1V-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_U1V-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/291e5b1a9f278f0833e8e1841ad0b1/1029_UQO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_UQO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/a2de86dc092e9617aa403656e10f54/1029_YZK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_YZK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/b2d28e749086010a4dc82b6ba75b21/1136_4EL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4EL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/a7c5647b1233bfddbf8926a2957a63/1136_70I-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_70I-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/c7e241948a43834d02788841de1c9b/1029_MYO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_MYO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/d360ecf51e7eca75366e0442e0756c/1136_5NI-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_5NI-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/b311165d33f0f7a606119e50e3812e/1047_KF-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_KF-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/de3819192cef82cb64c20f57735040/659_eRe-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_eRe-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/edb21235c859f7877453065e48e2d7/1136_574-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_574-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/886ca4e27f9ee393871a72cfc0bd61/1029_J3A-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_J3A-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/c4a93d85938ed785e00681ef5bea6f/1029_G3Y-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_G3Y-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/8902db1a4d533bd16f3f4e080debd9/1136_3UU-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3UU-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/2dc126895842a67c2c00b5b123c2bc/1047_N2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_N2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/95afa494a4bbbfa73270e913d7339e/1029_BPR1-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BPR1-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/27d2db8afa27f9122e893144d1ba22/1029_HPO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_HPO-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/3116621eeb718a829ff724abf3e723/1136_4GA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4GA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/b7335b7fccdcd30a6e250ef7f3cab3/1047_DA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_DA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/19ceed167e3bc2ba0f16864b36b0c3/1029_PC8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_PC8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/cba88943de5f7e6bdae2ba6ce64873/1047_GP-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_GP-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/e77e1a363b21d25ff0a9380a1b0310/1136_3IL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3IL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/afdb81651b1467ac04934766ebd93d/1136_2LY-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_2LY-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/33/c056ba1f6e40b07c45d6b0a95d40fa/manifest.tsv manifest.tsv")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/69fbd875261ca4954ad372825066d4/1029_IB4-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_IB4-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/9f56e1a869ccb2b5a21045ec1d1b6a/1136_3CS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3CS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a/.command.run .command.run")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/a07cc26d7c693f5be68c942b1b4091/1029_YGP-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_YGP-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/02b2898dba79901df47bb2896274d8/1136_6SL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_6SL-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/820a1dfb6d8262fdf113a7e7ca2445/1173_SK8-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz 1173_SK8-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/e6dfa2853fe7addc295797cd5f793c/1136_5TH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_5TH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/356a582bfdaae80893df8c26eb7487/1029_D3G-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_D3G-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/59e6d2bf41dec67db2945a63ac864b/1029_QN-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_QN-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/17fa178a53a17c6704e87a116948e1/1047_OE-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_OE-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/cd0684cc157c71f24a4b09e8a1cc40/1029_BPNX-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BPNX-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/303e65f164623fb84ebcd4ad16f92d/659_eNS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_eNS-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/76c241bda3f6819e9e8318702ccd26/1029_ICH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_ICH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/d2d17cde4d8e208ae06f1b7ab1639a/1136_80V-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_80V-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/22ff57fe39a08172cfd1205bfe0780/1136_6O2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_6O2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/c83184127c611613c3f81d03aff92a/1136_7F2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_7F2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/2c9dfff66bef12305c44bc5cd47b7a/1047_X-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_X-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/cd11a3928f4b3c92dfa984e48b876c/1136_4UT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4UT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/5ed71ade08eb0445de92edf99aac8c/659_dhR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_dhR-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/03f3f998f99ac1beb1485f3d3c33a3/1029_OSZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_OSZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/393cabc2a51de720ff0de59e55f805/1029_Q88-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_Q88-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/9391e4fe4364b08366e87a70c5e63b/1029_IT8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_IT8-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/099cd8083b1b781157d8c8d7cf35de/1029_W0T-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_W0T-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/7acd275d2aaeb310334eb4263ffce5/1029_BJND-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BJND-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/0dfe11b186a30ebe1ed6cf5cad3097/1029_R3S-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_R3S-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/606f78b5958307b23f710fbb6074a3/1136_8DJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_8DJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/a0719ec0cf33d4a71e2b628505d496/1029_V8X-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_V8X-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/f622ac91638b0e17d8997236dece7f/1047_K2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_K2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/18d1c24c44ee6ae89585e16e2932df/1173_FM-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz 1173_FM-N1-BDNA-01_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/c636feecd879b989c05486fc1e8853/1029_IWJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_IWJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/e567ca07ddb2ee53bc070a206717dc/1136_4S5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_4S5-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/2ad4fc37b4d4f6c678c10074f80c5f/1029_BKSJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_BKSJ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/b55df97a6dc6b561720f440f2d1fc2/1047_KV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_KV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/04d50afd3f4f70707f5bab077d5611/1047_MK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_MK-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/05a360d33d06449531ef8b34f01aa1/1029_I46-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_I46-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/86d63c8a4a4f6e037bd3662119bd2b/1136_5R2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_5R2-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/1c6c1a70fb1b459fce43dba2a310be/659_drH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_drH-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/667cd538d001ebb317dd0961c99216/659_cKj-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_cKj-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/0cf90b8888763a5667c5b1df26e54a/1136_3ZV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_3ZV-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/80a0a9075ba4c854e75ed9b694d997/659_bnZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_bnZ-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/f24ffc754ae62f7d1495b950228c62/1136_2JT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_2JT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/0de5f7fd274aadac6f9129bade5ead/1047_OC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_OC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/0983a4e3fc6b81a0a827dc36cb12f5/659_de0-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_de0-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/add203f743f7e4333ed7e5796abac0/1029_38M-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_38M-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/b79110c116b246da7d56a2a5242bbf/1029_W8F-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1029_W8F-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/2b32c635b209913037eedc36495ef1/1136_6FA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1136_6FA-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/23e7fa24c5549dff0de31300e6dd7c/659_cFT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_cFT-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/043e77f31b02c9feaca8a7d3fb74f9/659_hv-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 659_hv-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/413e2ce13ab83c65cc98890fb7e266/1047_KC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz 1047_KC-N1-BDNA-1_B23MHTGLT4_1_probes.tsv.gz")
    nxf_parallel "${downloads[@]}"
    echo "==> STAGING COMPLETE (185 inputs)"
    echo ""
}

nxf_unstage_outputs() {
    true
    uploads=()
    IFS=$'\n'
    for name in $(eval "ls -1d batch_reference.parquet sex_calls.csv feature_stats.csv versions.yml" | sort | uniq); do
        uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a")
    done
    unset IFS
    nxf_parallel "${uploads[@]}"
}

nxf_unstage_controls() {
    true
    nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a || true
    nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a || true
    nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/139bbe0f68100e9f7b0b0c5286096a || 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/df/139bbe0f68100e9f7b0b0c5286096a/.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