#!/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/30/f2f03a1d68f5f8721158aa811601c9/.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 869_XA6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_TVZ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_VG6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_IYA-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_b6L-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_sv-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_bu4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_OZL-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_U1S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_XTN-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_MJX-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_G7Y-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_NGX-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_csY-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_NNC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_NJC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_HUS-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_btT-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_esc-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_KTE-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_91-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f manifest.tsv
    rm -f 869_B0C-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_OC5-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f .command.run
    rm -f 869_ZJJ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_PEY-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_bPW-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_MMQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_eZ3-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_LRV-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_LWM-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f .command.sh
    rm -f 659_c6S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_QC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_XR8-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_BLV-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_bmI-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_EH0-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_SL4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_PRH-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_bHx-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_E6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 659_bD1-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_B0O-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_VZQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_GL8-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_B8Q-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    rm -f 869_YQB-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/451b13a415051f2608900280e3a2ef/869_XA6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_XA6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/ebe5e6fdd58be9b9c45f484d53757d/869_TVZ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_TVZ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/e5717996a7f286931d58beef2f13ca/869_VG6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_VG6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/c9fc37feb727fc78da3a325dd9bf1b/869_IYA-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_IYA-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/411ee9359b00c9ad84e8bdb04e999a/659_b6L-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_b6L-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/17196b9cc4a5cfb8f5c10e23b8caef/659_sv-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_sv-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/84dc9e8f0736549154734145f19b52/659_bu4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_bu4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/153475abd46188fdb4ee406a3d77e3/869_OZL-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_OZL-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/7f32cc9fb32b9f1a8218f21ee3176f/869_U1S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_U1S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/2d92fed81622fa0fdee4bb4a106882/869_XTN-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_XTN-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/9ee38266cf5ee268d2e6e0d2c3cec9/869_MJX-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_MJX-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/8c0906b7e120e3151a4cb155fb2b8a/869_G7Y-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_G7Y-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/d06203ec5b9e565f32d4bed28c0541/869_NGX-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_NGX-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/08d69c8d303d21ba45bb57065ceddb/659_csY-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_csY-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/27d85382aac6b599551fdf6efcb70a/869_NNC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_NNC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/4f2a536936431c767441df02383566/869_NJC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_NJC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/258ef2bdaa08997b0f9f447ca761d3/869_HUS-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_HUS-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/7fcbcad42cc5136adf5b5e8f02a2ce/659_btT-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_btT-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/03b7537fde43f16d00b6c68d10b9cd/659_esc-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_esc-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/7ceee94c2caef4817ae2218f1f1a51/869_KTE-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_KTE-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/c31f42b6f3e7e20f208d4d95d89715/659_91-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_91-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/60/9c482a92ebe6f6f913cb942dcd0228/manifest.tsv manifest.tsv")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/0c36bd52b2818d86214213f984aafa/869_B0C-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_B0C-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/46f3dec819e9d5e73fe83e9b53cca5/869_OC5-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_OC5-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9/.command.run .command.run")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/4a510aa9540137a18ae07506f02b3b/869_ZJJ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_ZJJ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/cc1586a67ccecaceb1f03495adc129/869_PEY-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_PEY-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/581e618e27f1d22b490579db97cabc/659_bPW-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_bPW-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/cdbe1c74b37045d732655932495918/869_MMQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_MMQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/9b8514ddc861ac7aa3b433ae0bf84c/659_eZ3-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_eZ3-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/8ec5d937f0c6524cbd5d91c9d954a2/869_LRV-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_LRV-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/2f22d250f3ca3f1a0ea297201a760d/869_LWM-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_LWM-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9/.command.sh .command.sh")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/96826b69e6afd41502db9c38fec79f/659_c6S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_c6S-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/bb52f4a3cc2453294fdebf77899fdc/659_QC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_QC-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/00e2eebcb8feb910bf274e7f099ca3/869_XR8-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_XR8-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/efabf15dba57296437cf2eeb7a6611/869_BLV-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_BLV-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/a98f88dcb38f6c6218a16ee803ad01/659_bmI-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_bmI-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/f4374b0029be97b5103588615b6d58/869_EH0-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_EH0-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/2df676a6c7e2d1076dfa6afc1f9f7e/869_SL4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_SL4-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/b325527fe0001c7dbe9b915cf754e1/869_PRH-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_PRH-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/fa87da294d2efce61c729bd82ac31e/659_bHx-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_bHx-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/2c1a128635c236d1ad50c04f617f74/869_E6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_E6-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/5ce3f9366bb0fddc72100a692314ac/659_bD1-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 659_bD1-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/639bc4a596c514a864d7e0f071fbfe/869_B0O-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_B0O-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/b2126d480b5f50d99d925d7fc231af/869_VZQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_VZQ-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/6f89b170946fa3090f698c867d2a6b/869_GL8-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_GL8-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/0c6feb3b78d799e52030547b014baa/869_B8Q-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_B8Q-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/8f810662562a7a92b0e44fb93f1975/869_YQB-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz 869_YQB-N1-BDNA-1_A23FG3YLT4_1_probes.tsv.gz")
    nxf_parallel "${downloads[@]}"
    echo "==> STAGING COMPLETE (49 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/30/f2f03a1d68f5f8721158aa811601c9")
    done
    unset IFS
    nxf_parallel "${uploads[@]}"
}

nxf_unstage_controls() {
    true
    nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9 || true
    nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9 || true
    nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f2f03a1d68f5f8721158aa811601c9 || 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/30/f2f03a1d68f5f8721158aa811601c9/.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