#!/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/9b/5b11715f761d1627fae83e19dedaa9/.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)
    rm -f 1136_2QY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_OFT-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1029_FSS-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_1VE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_42D-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_TB0-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_5BE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_3T4-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_KAF-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_03T-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_D36-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_7VJ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_6K6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_4DP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_4E9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_7L-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_K8V-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_3JH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_HV2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_65R-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1029_BTXK-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_CPH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_DNH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_77Q-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_HI8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_P6B-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_5PQ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_1I8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_2F2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1029_YCN-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_XYF-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_2E7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_ED4-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_7BW-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_0KC-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_6WU-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_2S9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_1VP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_5AH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_3I9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f manifest.tsv
    rm -f 869_VV1-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1029_PAP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_3FE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f .command.run
    rm -f 869_OMQ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_I3-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_3X6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_814-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_NTY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1029_XI2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_ROX-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_2RO-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f .command.sh
    rm -f 869_DOI-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_5JZ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_75V-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_42G-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_35B-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_6F7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_0L8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_5Z2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_YP6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_UZP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_RWW-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1029_BNK6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_FH7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_2PU-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_0QH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_7OO-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_VTY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 869_LSE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    rm -f 1136_3FA-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/70a45730b9cca4a67af2d287a679b9/1136_2QY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_2QY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/68f8e255563827aacab75bcb4e71a7/869_OFT-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_OFT-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/c3412b8e515ee35cb79ab36f0ca88f/1029_FSS-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1029_FSS-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/32a89f2973ac8efcc36a5251872d7d/1136_1VE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_1VE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/6515f1860bc1a19e08741ff3317475/1136_42D-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_42D-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/dc8121352897959385852d96fc3b30/869_TB0-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_TB0-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/0cf8b066bfc969f82c08a0981e3c66/1136_5BE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_5BE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b2e1c6257d583faad25cd887da6f88/1136_3T4-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_3T4-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/ed78b0f4eb615d1aeb337a30caedde/869_KAF-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_KAF-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/3c56a44fd1efffdfcf7041b28bf680/1136_03T-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_03T-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/54ba21f0961c7329bc8a822b9586aa/869_D36-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_D36-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/73607a17797b181b0b80673fd5ccb3/1136_7VJ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_7VJ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/543488546d3c0465bbcec475cb3611/1136_6K6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_6K6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/f9a273da607dd7c246c00f2d401b28/1136_4DP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_4DP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/26f3cf5fda482086b0fd788cd452a0/1136_4E9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_4E9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/360248dc7ab755b76ecb1df3dd9871/1136_7L-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_7L-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/a688b4a93e9f9ec232c20be4778d90/869_K8V-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_K8V-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/9d5f6f48c75637c2fa07518de9f983/1136_3JH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_3JH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/e8b3164e0a351a6ba2dba857bc4130/869_HV2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_HV2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/9af0247ee82e0b68044520d8bf7d56/1136_65R-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_65R-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/27e89849ccc530dd8d357312f7d121/1029_BTXK-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1029_BTXK-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/763fed8f7c3e741fe90c879997c9b1/869_CPH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_CPH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/6bc981791c430152a6bce7bc5232d6/869_DNH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_DNH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/53bcb86615171c7922971e8a2aa9d3/1136_77Q-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_77Q-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/91c3bf24725f304ef4eb510e6d6336/869_HI8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_HI8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/306af2f55f8063474942ec46828ce4/869_P6B-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_P6B-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/0dc356f2f08c622b8c0b20c7272763/1136_5PQ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_5PQ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/176a507de553986c8ad48913bc7bd8/1136_1I8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_1I8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/d71d0da983640e4ab38322bcabbf08/1136_2F2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_2F2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/72118cafd58d03d391d85454fd0f93/1029_YCN-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1029_YCN-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/d94b69f5e3d7510adc198c49ce0c7f/869_XYF-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_XYF-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/42bdc80b46a827786b0e9a0e72e188/1136_2E7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_2E7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/a43ced31f7661353afa3514a76565d/869_ED4-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_ED4-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/077bd2875e3b3da7d333ad938b0ea6/1136_7BW-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_7BW-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/883cabb9d086cd4ae508b09e9cd108/1136_0KC-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_0KC-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/20462bea4c83332d7d4d0f3ee6ef48/1136_6WU-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_6WU-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/500a78e14a0ee83305f9380b6a5870/1136_2S9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_2S9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/daa5c62d5be5b1263e6217bcd67070/1136_1VP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_1VP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/bbcddb6efb41af9fb9b4c2a0a83c24/1136_5AH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_5AH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/84eaeecd7de2104e1c6122920c5645/1136_3I9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_3I9-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/84/39203127936ae4f8fdb3abb6f1cac4/manifest.tsv manifest.tsv")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/bca23291a4f09a6c3df247b9444493/869_VV1-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_VV1-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/3eddbb350da3ec3861359cb5d37a0e/1029_PAP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1029_PAP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/f47f8c0aa104a516260ccba3340a9d/1136_3FE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_3FE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/5b11715f761d1627fae83e19dedaa9/.command.run .command.run")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/6309f8e49890ddbe9262586ee40302/869_OMQ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_OMQ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/8ced17e75dbadaeb129d1d0e961b7a/869_I3-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_I3-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/4c65b41cc14a4db43c2e49d460661a/1136_3X6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_3X6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/b1844d26672f5eace3f7acb5004a91/1136_814-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_814-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/a2ab6f69f94368d57754a50bb5bc09/869_NTY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_NTY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/0ea98ff1af352a2cc637af8a59c0af/1029_XI2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1029_XI2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/e373aeb7bc51bc71ed07b4076f1969/869_ROX-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_ROX-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/d0c0a63422f0ae83483ec9c9c4637a/1136_2RO-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_2RO-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/5b11715f761d1627fae83e19dedaa9/.command.sh .command.sh")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/bc60c169693496dc2575b72b3a2731/869_DOI-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_DOI-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/d31cd06cd9a82feef706fb1254dc0e/1136_5JZ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_5JZ-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/8a678ecbad45df2329e4305e19b158/1136_75V-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_75V-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/8a9d3e2fdbfbde6d7542f3b741b46e/1136_42G-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_42G-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/432ab851d8c757b3c4e955348b0509/1136_35B-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_35B-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/50e0e2225450ddeca1f487d5e7ee69/1136_6F7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_6F7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/45c0ce291737b41599c635fe0bea47/1136_0L8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_0L8-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/b2d6960c6d2ac95906d24c4c76d419/1136_5Z2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_5Z2-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/c324078b0677270ca35c2f9c517034/869_YP6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_YP6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/43c4b87b0e0b6b6976bf06d53ac638/869_UZP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_UZP-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/b03df9929999314634361e6bd07f71/869_RWW-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_RWW-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/9abc690950cd19dbc2597b765c2ac9/1029_BNK6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1029_BNK6-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/8799ea34eaf617ad3afa62fa31df95/869_FH7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_FH7-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/dbc8abb75684bc44a52a2be2f492af/1136_2PU-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_2PU-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/bc7393e70feb4eb4807413b280bfb2/1136_0QH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_0QH-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/3fef3d8a5ff69a91e9774b5c2a15a6/1136_7OO-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_7OO-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/a2c4e86cd0bc70896d80500b862400/869_VTY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_VTY-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/16a6997424e6587b69acf44ce61e73/869_LSE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 869_LSE-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/2be86299acd03fa04b6e38927e429e/1136_3FA-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz 1136_3FA-N1-BDNA-1_A237CFYLT3_1_probes.tsv.gz")
    nxf_parallel "${downloads[@]}"
    echo "==> STAGING COMPLETE (73 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/9b/5b11715f761d1627fae83e19dedaa9")
    done
    unset IFS
    nxf_parallel "${uploads[@]}"
}

nxf_unstage_controls() {
    true
    nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/5b11715f761d1627fae83e19dedaa9 || true
    nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/5b11715f761d1627fae83e19dedaa9 || true
    nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/5b11715f761d1627fae83e19dedaa9 || 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/9b/5b11715f761d1627fae83e19dedaa9/.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