#!/bin/bash
### ---
### name: 'DAQ:AGGREGATE_POSTDEDUP_QC (postdedup_qc_aggregation)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/aggregate_postdedup_qc:1.8.0'
### outputs:
### - 'postdedup_qc.json'
### - '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/a3/e88a98d9a4067a6e5513b0aca058be/.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 HCC1395_BL_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood.sentieon.insert_size_metrics
rm -f HCC1395_tumor.sentieon.insert_size_metrics
rm -f HCC1395_BL.mosdepth.summary.txt
rm -f HCC1395_BL_foresight_clarity_targets_hg38.sentieon.hs_metrics
rm -f HCC1395_BL_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood.stats
rm -f HCC1395_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f HCC1395_BL_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics
rm -f Sig_18_tissue_foresight_clarity_targets_hg38.sentieon.hs_metrics
rm -f HCC1395_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics
rm -f HCC1395_tumor.stats
rm -f Sig_18_tissue_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
rm -f Sig_18_tissue.mosdepth.summary.txt
rm -f Sig_18_tissue.sentieon.insert_size_metrics
rm -f Sig_18_tissue_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_tissue_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_tissue_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics
rm -f HCC1395_tumor.mosdepth.summary.txt
rm -f Sig_18_Blood_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood.mosdepth.summary.txt
rm -f HCC1395_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
rm -f .command.run
rm -f Sig_18_Blood_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
rm -f HCC1395_BL_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
rm -f Sig_18_tissue_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood_foresight_clarity_targets_hg38.sentieon.hs_metrics
rm -f Sig_18_tissue_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
rm -f Sig_18_Blood_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics
rm -f .command.sh
rm -f HCC1395_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
rm -f HCC1395_BL.stats
rm -f HCC1395_BL.sentieon.insert_size_metrics
rm -f Sig_18_tissue.stats
rm -f HCC1395_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics
rm -f Sig_18_Blood_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
rm -f HCC1395_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_Blood_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f Sig_18_tissue_full_basic_stats.tsv
rm -f HCC1395_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics
rm -f HCC1395_BL_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
rm -f HCC1395_BL_full_basic_stats.tsv
rm -f HCC1395_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
rm -f HCC1395_BL_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
rm -f HCC1395_tumor_full_basic_stats.tsv
rm -f HCC1395_BL_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
rm -f Sig_18_Blood_full_basic_stats.tsv
rm -f Sig_18_tissue_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/e92662f53909ff4db354575fa4d9d2/HCC1395_BL_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics HCC1395_BL_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/17c3c02857a2c93b826b865aa481e4/Sig_18_Blood_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics Sig_18_Blood_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/97e37b1c619f2c369e709c06c53ed4/Sig_18_Blood.sentieon.insert_size_metrics Sig_18_Blood.sentieon.insert_size_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/2c6b5990e9a11787cfd337594154c5/HCC1395_tumor.sentieon.insert_size_metrics HCC1395_tumor.sentieon.insert_size_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/61e1ef50a070fc433472b7e9850037/HCC1395_BL.mosdepth.summary.txt HCC1395_BL.mosdepth.summary.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/1fbfeb0e0affadb3006fda9ba40614/HCC1395_BL_foresight_clarity_targets_hg38.sentieon.hs_metrics HCC1395_BL_foresight_clarity_targets_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/beca13b2838c7bc782dfaecc2d28e6/HCC1395_BL_altera_v3_targets_postQC_hg38.sentieon.hs_metrics HCC1395_BL_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/399af6134a4146e3e3d5264f87c5ae/Sig_18_Blood.stats Sig_18_Blood.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/d6e49a79a8670df1a0d4e094700d35/HCC1395_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics HCC1395_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/546f04f92f89559381a48ad0b52ed8/HCC1395_BL_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics HCC1395_BL_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/12fe80f4ea4443d36aa8eb718ad42f/Sig_18_tissue_foresight_clarity_targets_hg38.sentieon.hs_metrics Sig_18_tissue_foresight_clarity_targets_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/d73ff583418d1e12a0ca1f34327271/HCC1395_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics HCC1395_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/d15ececd85b7f2e0be6d5d020db2a8/HCC1395_tumor.stats HCC1395_tumor.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/5143b29b9204a26d261e1d5e708e65/Sig_18_tissue_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics Sig_18_tissue_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/c477930629e0213808b081ec04aa17/Sig_18_tissue.mosdepth.summary.txt Sig_18_tissue.mosdepth.summary.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/9ba9308eaab301cc457cc0e38af99c/Sig_18_tissue.sentieon.insert_size_metrics Sig_18_tissue.sentieon.insert_size_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/45785fdbcff1d286ececa3e29e3d54/Sig_18_tissue_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics Sig_18_tissue_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/e71a5abd02b243e08a5fc40bc38f45/Sig_18_tissue_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics Sig_18_tissue_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/031f997fcbfebb2d93b85dc4313caa/Sig_18_tissue_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics Sig_18_tissue_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/8e0fbf91e51be4787a5634b3944370/HCC1395_tumor.mosdepth.summary.txt HCC1395_tumor.mosdepth.summary.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/bddaf78aae9b2589ffbcc04bbadc4b/Sig_18_Blood_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics Sig_18_Blood_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/18500304ee45c4ddb3c56530e0db78/Sig_18_Blood.mosdepth.summary.txt Sig_18_Blood.mosdepth.summary.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/6930d69dfddf2da77bf640bc2d64b5/HCC1395_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics HCC1395_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/e88a98d9a4067a6e5513b0aca058be/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/b9d597cd3da9738b600baf7a8f1d28/Sig_18_Blood_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics Sig_18_Blood_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/cdfb388df2460e26b027da1c43167c/HCC1395_BL_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics HCC1395_BL_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/627efe14c0d2d00f335011102a16e8/Sig_18_tissue_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics Sig_18_tissue_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/d8e2fc779c652252a9cc73b0404abb/Sig_18_Blood_foresight_clarity_targets_hg38.sentieon.hs_metrics Sig_18_Blood_foresight_clarity_targets_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/56542f0b2f431b371b202500bb701e/Sig_18_tissue_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics Sig_18_tissue_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/f4519361665682196a7978d76a9cd4/Sig_18_Blood_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics Sig_18_Blood_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/e88a98d9a4067a6e5513b0aca058be/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/289e51e836a74e9f6195c6129a89dc/HCC1395_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics HCC1395_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/0826b36088ab827cc986ae7be8a9ab/HCC1395_BL.stats HCC1395_BL.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/989e16d387b4c390c6ab2f9542d41d/HCC1395_BL.sentieon.insert_size_metrics HCC1395_BL.sentieon.insert_size_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/207bf035287a101d0e8ddf9a2352fa/Sig_18_tissue.stats Sig_18_tissue.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/1d6e66a3f0cad5e6f56ea0de883462/HCC1395_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics HCC1395_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/5b0c5b82fc186f664d4e8724447585/Sig_18_Blood_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics Sig_18_Blood_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/a1cf5a6af3b53e281a8b4ef63ab564/Sig_18_Blood_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics Sig_18_Blood_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/8acca88d290a2f4df768c581c681e4/HCC1395_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics HCC1395_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/94a65f7ba4dc181a3c41831dcc7437/Sig_18_Blood_altera_v3_targets_postQC_hg38.sentieon.hs_metrics Sig_18_Blood_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/5fe3d43337a478be56be39fe611b33/Sig_18_tissue/Sig_18_tissue_full_basic_stats.tsv Sig_18_tissue_full_basic_stats.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/4975cf3b64b9f224999762a5f7d295/HCC1395_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics HCC1395_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/0f1c94e7ba75892f57b4e3740ca760/HCC1395_BL_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics HCC1395_BL_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/cce4df4c219cbcdf9786114aeb445a/HCC1395_BL/HCC1395_BL_full_basic_stats.tsv HCC1395_BL_full_basic_stats.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/a7d1d4b5bd4d8c8566ef59cc77d4bb/HCC1395_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics HCC1395_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/a8fba1f54300b815527327e59b0f6a/HCC1395_BL_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics HCC1395_BL_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/65312c3722acf1c30f933193c461b8/HCC1395_tumor/HCC1395_tumor_full_basic_stats.tsv HCC1395_tumor_full_basic_stats.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/89a1960f9e1085a012f5e192a8561c/HCC1395_BL_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics HCC1395_BL_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/ba0359a8bcc9c83f354fa51ce2c49e/Sig_18_Blood/Sig_18_Blood_full_basic_stats.tsv Sig_18_Blood_full_basic_stats.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/cb768976e03ee86a6838df554ebee5/Sig_18_tissue_altera_v3_targets_postQC_hg38.sentieon.hs_metrics Sig_18_tissue_altera_v3_targets_postQC_hg38.sentieon.hs_metrics")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (50 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d postdedup_qc.json versions.yml" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/e88a98d9a4067a6e5513b0aca058be")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/e88a98d9a4067a6e5513b0aca058be || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/e88a98d9a4067a6e5513b0aca058be || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/e88a98d9a4067a6e5513b0aca058be || 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/a3/e88a98d9a4067a6e5513b0aca058be/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/29/affdc163cec89b3ca5710c403314b4/bin/*" $NXF_SCRATCH/nextflow-bin/
chmod +x $NXF_SCRATCH/nextflow-bin/* || true
export PATH=$NXF_SCRATCH/nextflow-bin:$PATH
[[ $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