#!/bin/bash
#SBATCH -J nf-NFCORE_ATACSEQ_ATACSEQ_MERGED_LIBRARY_CONSENSUS_PEAKS_MACS3_CONSENSUS_(consensus_peaks)
#SBATCH -o /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b/.command.log
#SBATCH --no-requeue
#SBATCH --signal B:USR2@30
#SBATCH -t 20:00:00
#SBATCH --mem 6144M
#SBATCH -p fast
NXF_CHDIR=/shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b
### ---
### name: 'NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_CONSENSUS_PEAKS:MACS3_CONSENSUS (consensus_peaks)'
### container: '/shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24-5d182f583f4696f4c4d9f3be93052811b383341f-0.img'
### outputs:
### - '*.bed'
### - '*.saf'
### - '*.pdf'
### - '*.boolean.txt'
### - '*.intersect.txt'
### - '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)

    /usr/bin/env bash -C -e -u -o pipefail /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b/.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
    
    /usr/bin/env bash -C -e -u -o pipefail /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b/.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
}
# aws cli retry config
export AWS_RETRY_MODE=standard 
export AWS_MAX_ATTEMPTS=5
# aws helper
nxf_s3_upload() {
    local name=$1
    local s3path=$2
    if [[ "$name" == - ]]; then
      aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
    elif [[ -d "$name" ]]; then
      aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
    else
      aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
    fi
}

nxf_s3_download() {
    local source=$1
    local target=$2
    local file_name=$(basename $1)
    local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
    if [[ $is_dir == 1 ]]; then
        aws s3 cp --only-show-errors --recursive "$source" "$target"
    else 
        aws s3 cp --only-show-errors "$source" "$target"
    fi
}
nxf_container_env() {
cat << EOF
export PYTHONNOUSERSITE="1"
export R_PROFILE_USER="/.Rprofile"
export R_ENVIRON_USER="/.Renviron"
export JULIA_DEPOT_PATH="/usr/local/share/julia"
export PATH="\$PATH:/shared/home/rcoux/.nextflow/assets/nf-core/atacseq/bin"
EOF
}

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 > /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b/.exitcode
    set +u
    exit $exit_status
}

on_term() {
    set +e
    [[ "$pid" ]] && nxf_kill $pid
}

nxf_launch() {
    set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-home --pid -B /shared -B /shared /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24-5d182f583f4696f4c4d9f3be93052811b383341f-0.img /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_container_env); bash -C -e -u -o pipefail /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b/.command.run nxf_trace"
}

nxf_stage() {
    true
    # stage input files
    rm -f FO_TLR997_REP3.mLb.clN_peaks.narrowPeak
    rm -f FO_WT_REP1.mLb.clN_peaks.narrowPeak
    rm -f MZ_TLR997_REP1.mLb.clN_peaks.narrowPeak
    rm -f ABC_WT_REP3.mLb.clN_peaks.narrowPeak
    rm -f Mem_REP1.mLb.clN_peaks.narrowPeak
    rm -f YFP_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_TLR997_REP3.mLb.clN_peaks.narrowPeak
    rm -f ABC_b_REP2.mLb.clN_peaks.narrowPeak
    rm -f FO_TLR997_REP1.mLb.clN_peaks.narrowPeak
    rm -f ABC_WT_REP1.mLb.clN_peaks.narrowPeak
    rm -f FO_TRL9_het_REP3.mLb.clN_peaks.narrowPeak
    rm -f D3B_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_TLR997_REP1.mLb.clN_peaks.narrowPeak
    rm -f ABC_TLR9_het_REP1.mLb.clN_peaks.narrowPeak
    rm -f MCH_REP4.mLb.clN_peaks.narrowPeak
    rm -f ABC_TLR9_het_REP3.mLb.clN_peaks.narrowPeak
    rm -f ABC_TLR997_REP2.mLb.clN_peaks.narrowPeak
    rm -f YFP_REP3.mLb.clN_peaks.narrowPeak
    rm -f Mem6h_REP1.mLb.clN_peaks.narrowPeak
    rm -f NB_REP2.mLb.clN_peaks.narrowPeak
    rm -f YFP_REP4.mLb.clN_peaks.narrowPeak
    rm -f D3B_REP1.mLb.clN_peaks.narrowPeak
    rm -f ABC_TLR9_het_REP2.mLb.clN_peaks.narrowPeak
    rm -f MCH_REP3.mLb.clN_peaks.narrowPeak
    rm -f MZ_TLR9_het_REP1.mLb.clN_peaks.narrowPeak
    rm -f Mem6h_REP2.mLb.clN_peaks.narrowPeak
    rm -f MZ_TLR9_het_REP2.mLb.clN_peaks.narrowPeak
    rm -f MCH_REP2.mLb.clN_peaks.narrowPeak
    rm -f Mem_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_a_REP2.mLb.clN_peaks.narrowPeak
    rm -f FO_TRL9_het_REP1.mLb.clN_peaks.narrowPeak
    rm -f NB_REP1.mLb.clN_peaks.narrowPeak
    rm -f FO_TRL9_het_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_a_REP1.mLb.clN_peaks.narrowPeak
    rm -f MCH_REP1.mLb.clN_peaks.narrowPeak
    rm -f MZ_TLR997_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_WT_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_b_REP1.mLb.clN_peaks.narrowPeak
    rm -f FO_TLR997_REP2.mLb.clN_peaks.narrowPeak
    rm -f ABC_b_REP3.mLb.clN_peaks.narrowPeak
    rm -f YFP_REP1.mLb.clN_peaks.narrowPeak
    rm -f BiA_REP4.mLb.clN_peaks.narrowPeak
    rm -f MZ_WT_REP3.mLb.clN_peaks.narrowPeak
    rm -f MZ_WT_REP2.mLb.clN_peaks.narrowPeak
    rm -f MZ_WT_REP1.mLb.clN_peaks.narrowPeak
    rm -f BiA_REP1.mLb.clN_peaks.narrowPeak
    rm -f FO_WT_REP3.mLb.clN_peaks.narrowPeak
    rm -f BiA_REP2.mLb.clN_peaks.narrowPeak
    rm -f NB6h_REP2.mLb.clN_peaks.narrowPeak
    rm -f FO_WT_REP2.mLb.clN_peaks.narrowPeak
    rm -f MZ_TLR997_REP3.mLb.clN_peaks.narrowPeak
    rm -f NB6h_REP1.mLb.clN_peaks.narrowPeak
    rm -f BiA_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/3e/4d1aee448494a02e07f589834b04e9/FO_TLR997_REP3.mLb.clN_peaks.narrowPeak FO_TLR997_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2b/49cd3a515d8310947d35c102efb892/FO_WT_REP1.mLb.clN_peaks.narrowPeak FO_WT_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/87/83ac584e6ea2a5b63b9047798f4c72/MZ_TLR997_REP1.mLb.clN_peaks.narrowPeak MZ_TLR997_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/da/64326301b3f372034a1895173844bf/ABC_WT_REP3.mLb.clN_peaks.narrowPeak ABC_WT_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/0b/4d1cb9658f35eaf458df76a903b17e/Mem_REP1.mLb.clN_peaks.narrowPeak Mem_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/8d/189d769f6d1ccce38526ff65071cee/YFP_REP2.mLb.clN_peaks.narrowPeak YFP_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/b9/a0b49654e96643445a13b200bfce2e/ABC_TLR997_REP3.mLb.clN_peaks.narrowPeak ABC_TLR997_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/80/100bc71bd012bc2daae572c9c91c8f/ABC_b_REP2.mLb.clN_peaks.narrowPeak ABC_b_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/c1/dbbc7004c516e686f5c74991802ec2/FO_TLR997_REP1.mLb.clN_peaks.narrowPeak FO_TLR997_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/28/8c50cf3d36bf9ccaa942ea0f7b47c5/ABC_WT_REP1.mLb.clN_peaks.narrowPeak ABC_WT_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/23/ba85da0ced03bf0eba76ce013b2806/FO_TRL9_het_REP3.mLb.clN_peaks.narrowPeak FO_TRL9_het_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/91/2f01b78ba7b518f5aa4e62f8b5f53b/D3B_REP2.mLb.clN_peaks.narrowPeak D3B_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/ee/966a0badc22fbec4ab9f1671982625/ABC_TLR997_REP1.mLb.clN_peaks.narrowPeak ABC_TLR997_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/fe/4de3ca20678df0ffa23e918bd263e0/ABC_TLR9_het_REP1.mLb.clN_peaks.narrowPeak ABC_TLR9_het_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/3c/1c1665b29d3cfc9ea9c13e332e9bb9/MCH_REP4.mLb.clN_peaks.narrowPeak MCH_REP4.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/df/c232966280a13828492850513af0d5/ABC_TLR9_het_REP3.mLb.clN_peaks.narrowPeak ABC_TLR9_het_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/c6/0dda81b66c2bc35db2a74ae78984e0/ABC_TLR997_REP2.mLb.clN_peaks.narrowPeak ABC_TLR997_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/40/bf2a06928017275544a62224b40362/YFP_REP3.mLb.clN_peaks.narrowPeak YFP_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/dd/914c622edf39a11b9e527583739110/Mem6h_REP1.mLb.clN_peaks.narrowPeak Mem6h_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/1c/8b3b117314d1c9c10006d1f89651a9/NB_REP2.mLb.clN_peaks.narrowPeak NB_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/30/bb0b999ad9d8c6bb635e4abd3aaa6d/YFP_REP4.mLb.clN_peaks.narrowPeak YFP_REP4.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/3e/06bd4f1656256d2dc8e0dd6e4c5676/D3B_REP1.mLb.clN_peaks.narrowPeak D3B_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/b9/63695ea7847f7cd5df34c4db917d43/ABC_TLR9_het_REP2.mLb.clN_peaks.narrowPeak ABC_TLR9_het_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/f6/349a6e87c866e7c0f42fb0c604c586/MCH_REP3.mLb.clN_peaks.narrowPeak MCH_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/8a/c72bcd3de5c7da677c92ad54a82b8d/MZ_TLR9_het_REP1.mLb.clN_peaks.narrowPeak MZ_TLR9_het_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/4b/46399d03544efe5f3c9e7070329ca3/Mem6h_REP2.mLb.clN_peaks.narrowPeak Mem6h_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/1a/6d58ba0a38d7d19d6c1cb2dd1c5235/MZ_TLR9_het_REP2.mLb.clN_peaks.narrowPeak MZ_TLR9_het_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/fd/e50e229d6381c827fde32c9fc9954a/MCH_REP2.mLb.clN_peaks.narrowPeak MCH_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/09/a45ae32c0166cfefd1c7afb2d56c7e/Mem_REP2.mLb.clN_peaks.narrowPeak Mem_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/e7/9b7050d23a0616eea9e4f1675a8e83/ABC_a_REP2.mLb.clN_peaks.narrowPeak ABC_a_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/c9/1493a3c57e5e6a76d9a68f2c601573/FO_TRL9_het_REP1.mLb.clN_peaks.narrowPeak FO_TRL9_het_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/17/aca7aac1ca1cd11d04aecad72ae70e/NB_REP1.mLb.clN_peaks.narrowPeak NB_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/39/3f1fb4ff88c46a27c21f164d0d56be/FO_TRL9_het_REP2.mLb.clN_peaks.narrowPeak FO_TRL9_het_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/c9/227100f872c84b9f8d5ed04b0837bc/ABC_a_REP1.mLb.clN_peaks.narrowPeak ABC_a_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/da/85fad0d3c0c4950ac246ade4538656/MCH_REP1.mLb.clN_peaks.narrowPeak MCH_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/93/6707412cfe0db592d8ff500e61e2be/MZ_TLR997_REP2.mLb.clN_peaks.narrowPeak MZ_TLR997_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/7f/501d787f333ea6fafe924e8182e2f9/ABC_WT_REP2.mLb.clN_peaks.narrowPeak ABC_WT_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/08/f59e54d5253b8a023d44b6187a5968/ABC_b_REP1.mLb.clN_peaks.narrowPeak ABC_b_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/a6/47f34aaa75288986d82fcd4cb0d91c/FO_TLR997_REP2.mLb.clN_peaks.narrowPeak FO_TLR997_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/79/6eece98698c1913d02f3cc1685a7eb/ABC_b_REP3.mLb.clN_peaks.narrowPeak ABC_b_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/bc/b42a32c17ba5f2069cf1bdf59285f3/YFP_REP1.mLb.clN_peaks.narrowPeak YFP_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/6c/21fd9a83ab976551eefff16d4e3657/BiA_REP4.mLb.clN_peaks.narrowPeak BiA_REP4.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/67/5b13df8ee993bcb62079ba185c5d19/MZ_WT_REP3.mLb.clN_peaks.narrowPeak MZ_WT_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2e/0985cc769884675205a966414fcd5d/MZ_WT_REP2.mLb.clN_peaks.narrowPeak MZ_WT_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/4a/29cc75ca0d06724840c37749953759/MZ_WT_REP1.mLb.clN_peaks.narrowPeak MZ_WT_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/a6/95fb6e9bd5b861c476065b30c0a56d/BiA_REP1.mLb.clN_peaks.narrowPeak BiA_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/1d/d4d7b92087155606cc64bacfc1c513/FO_WT_REP3.mLb.clN_peaks.narrowPeak FO_WT_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/3f/1b568cd4aae5110ffe521351902e75/BiA_REP2.mLb.clN_peaks.narrowPeak BiA_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/e9/b9f9c08d1fc95bef912df19307dc2a/NB6h_REP2.mLb.clN_peaks.narrowPeak NB6h_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/64/ef4a90a9d868adab92aa415959a86e/FO_WT_REP2.mLb.clN_peaks.narrowPeak FO_WT_REP2.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/e0/6bae03ffcca512eb99f26376a9453c/MZ_TLR997_REP3.mLb.clN_peaks.narrowPeak MZ_TLR997_REP3.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/ad/caef57be367000731fc5edcd260802/NB6h_REP1.mLb.clN_peaks.narrowPeak NB6h_REP1.mLb.clN_peaks.narrowPeak
    ln -s /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/d5/9beefac4f9925bd1ee3697f9e19807/BiA_REP3.mLb.clN_peaks.narrowPeak BiA_REP3.mLb.clN_peaks.narrowPeak
}

nxf_unstage_outputs() {
    true
}

nxf_unstage_controls() {
    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"
    export NXF_BOXID="nxf-$(dd bs=18 count=1 if=/dev/urandom 2>/dev/null | base64 | tr +/ 0A | tr -d '\r\n')"
    NXF_SCRATCH=''
    [[ $NXF_DEBUG > 0 ]] && nxf_env
    touch /shared/ifbstor1/projects/nbl_nc_o4/ATAC_RX/ATAC_all/work/2d/c94b1c1d0db925e6cbe2c25066624b/.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