#!/bin/bash
### ---
### name: 'NIPT_CALLING:CONCAT_VCFS (2026-0073_HG00733_HG00732_FF_20)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/community.wave.seqera.io/library/htslib_pysam_numpy_scipy:275cef53a6366c67'
### outputs:
### - '2026-0073_HG00733_HG00732_FF_20.vcf'
### ...
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 -euo 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 $mem_proc' ERR
/bin/bash -euo pipefail .command.sh &
local task=$!
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/eb/77f85489ecb55fd8ef27bcd8be994c/.exitcode || true
set +u
rm -rf $NXF_SCRATCH || true
exit $exit_status
}
on_term() {
set +e
[[ "$pid" ]] && nxf_kill $pid
}
nxf_launch() {
/bin/bash -euo pipefail .command.run nxf_trace
}
nxf_stage() {
true
# stage input files
downloads=(true)
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0019.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0044.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0036.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0010.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0027.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0001.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0026.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0018.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0009.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0034.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0035.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0017.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0043.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0025.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0038.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0008.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0042.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0012.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0007.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0037.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0011.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0041.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0024.vcf
rm -f .command.run
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0031.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0006.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0022.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0023.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0005.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0040.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0014.vcf
rm -f .command.sh
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0021.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0048.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0047.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0030.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0004.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0039.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0013.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0046.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0033.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0020.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0016.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0003.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0029.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0002.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0032.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0045.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0015.vcf
rm -f 2026-0073_HG00733_HG00732_FF_20_shard_0028.vcf
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/6ce443ac4816f714172a41d2b2ac42/2026-0073_HG00733_HG00732_FF_20_shard_0019.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0019.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/48c0ce5a6eb9d92b31d094a661aa19/2026-0073_HG00733_HG00732_FF_20_shard_0044.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0044.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/510c83d99746c043bb0781bb7437fc/2026-0073_HG00733_HG00732_FF_20_shard_0036.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0036.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/65b675606016f8c4bb98881ceddf29/2026-0073_HG00733_HG00732_FF_20_shard_0010.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0010.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/f406975a5a4e7af0db41c584d4bc38/2026-0073_HG00733_HG00732_FF_20_shard_0027.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0027.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/6422f028f2b570be5f6a9ae672c38e/2026-0073_HG00733_HG00732_FF_20_shard_0001.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0001.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/10405c426cf41fae78fba1a53170fc/2026-0073_HG00733_HG00732_FF_20_shard_0026.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0026.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/b88155da173341e523c23e6baec84d/2026-0073_HG00733_HG00732_FF_20_shard_0018.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0018.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/9f5ebdb7934190ca3dd4b77dcf667a/2026-0073_HG00733_HG00732_FF_20_shard_0009.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0009.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/edea896f3ea953a074cb9fee61149d/2026-0073_HG00733_HG00732_FF_20_shard_0034.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0034.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/6d153e6954db09a8af38025879bdc6/2026-0073_HG00733_HG00732_FF_20_shard_0035.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0035.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/c45a3136e213c8a89669a0bb9bc5d9/2026-0073_HG00733_HG00732_FF_20_shard_0017.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0017.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/5fe436fb0bd78d43b1715139900f56/2026-0073_HG00733_HG00732_FF_20_shard_0043.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0043.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/a4fb64ac8184705e8d1a87ad592781/2026-0073_HG00733_HG00732_FF_20_shard_0025.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0025.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/7ff1fc7cbcccfb330c8da02bedd74c/2026-0073_HG00733_HG00732_FF_20_shard_0038.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0038.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/fa93d50830ff47026b572576eff053/2026-0073_HG00733_HG00732_FF_20_shard_0008.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0008.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/7bf668dfd313f3d53ca7bb149b4562/2026-0073_HG00733_HG00732_FF_20_shard_0042.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0042.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/62421bed823503f467a8f4d79b1daa/2026-0073_HG00733_HG00732_FF_20_shard_0012.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0012.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/11de21878a5bef2a58fa7c40fe5272/2026-0073_HG00733_HG00732_FF_20_shard_0007.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0007.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/1607866ac4933bdfcaf99e2c107f7a/2026-0073_HG00733_HG00732_FF_20_shard_0037.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0037.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/a6872236dc33ff3ca9bb3597ae75d3/2026-0073_HG00733_HG00732_FF_20_shard_0011.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0011.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/cf2e6be621ddfbe180fbb6e8b45d5f/2026-0073_HG00733_HG00732_FF_20_shard_0041.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0041.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/d947da969619a4351a55b94a15fa43/2026-0073_HG00733_HG00732_FF_20_shard_0024.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0024.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/77f85489ecb55fd8ef27bcd8be994c/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/d8bebc4b0525d23317f154301b43e8/2026-0073_HG00733_HG00732_FF_20_shard_0031.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0031.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/98da1065e017390bb3bf17474d8be1/2026-0073_HG00733_HG00732_FF_20_shard_0006.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0006.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/c0f6c5cbca74f80fcd6506af2624d1/2026-0073_HG00733_HG00732_FF_20_shard_0022.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0022.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/6871b4b7d0392ca3cd08ab778982dd/2026-0073_HG00733_HG00732_FF_20_shard_0023.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0023.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/51f0eec8d9bed7ec14db9d1fce5aa3/2026-0073_HG00733_HG00732_FF_20_shard_0005.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0005.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/52ad658a459369af28cd8ebbd65bf4/2026-0073_HG00733_HG00732_FF_20_shard_0040.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0040.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/03509574015fc0ae4009a2eaed078a/2026-0073_HG00733_HG00732_FF_20_shard_0014.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0014.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/77f85489ecb55fd8ef27bcd8be994c/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/94ebdedf83bff8223ba5e771c632c6/2026-0073_HG00733_HG00732_FF_20_shard_0021.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0021.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/07aa4c1788c3323243991e97c0d687/2026-0073_HG00733_HG00732_FF_20_shard_0048.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0048.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/a37a105c166ba4c95f61790997c990/2026-0073_HG00733_HG00732_FF_20_shard_0047.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0047.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/dc06d8f2530360ae08da64453bd9c8/2026-0073_HG00733_HG00732_FF_20_shard_0030.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0030.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/d2d667b3a57d8a87d1623228157c2f/2026-0073_HG00733_HG00732_FF_20_shard_0004.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0004.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/a4524718091564bba895800f69763e/2026-0073_HG00733_HG00732_FF_20_shard_0039.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0039.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/eded1fc4e84988a22969f1b51a9466/2026-0073_HG00733_HG00732_FF_20_shard_0013.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0013.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/a0975553861f67c140283085f8294c/2026-0073_HG00733_HG00732_FF_20_shard_0046.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0046.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/407b355afb1a02aee07c761533f235/2026-0073_HG00733_HG00732_FF_20_shard_0033.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0033.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/296d63792ce724c450896d81df1a7e/2026-0073_HG00733_HG00732_FF_20_shard_0020.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0020.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/7adfe5f8c32764372261b69ae48d5e/2026-0073_HG00733_HG00732_FF_20_shard_0016.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0016.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/c014cc707c2db570d341f121ccef25/2026-0073_HG00733_HG00732_FF_20_shard_0003.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0003.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/d307d0126c5c3ba35f3a83f720f6a3/2026-0073_HG00733_HG00732_FF_20_shard_0029.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0029.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/59af87b7d7c932659ae458d07134a5/2026-0073_HG00733_HG00732_FF_20_shard_0002.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0002.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/d5bfdb4775788b37ba190c6882d8aa/2026-0073_HG00733_HG00732_FF_20_shard_0032.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0032.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/46cba3c64c984a7545a46a7d5f6f83/2026-0073_HG00733_HG00732_FF_20_shard_0045.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0045.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/393a7fd37113ab52090972432fd47e/2026-0073_HG00733_HG00732_FF_20_shard_0015.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0015.vcf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/cc172aef2ee809012e39d53e560aca/2026-0073_HG00733_HG00732_FF_20_shard_0028.vcf 2026-0073_HG00733_HG00732_FF_20_shard_0028.vcf")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (50 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d 2026-0073_HG00733_HG00732_FF_20.vcf" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/77f85489ecb55fd8ef27bcd8be994c")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/77f85489ecb55fd8ef27bcd8be994c || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/77f85489ecb55fd8ef27bcd8be994c || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/77f85489ecb55fd8ef27bcd8be994c || 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/eb/77f85489ecb55fd8ef27bcd8be994c/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/38/7e191f9845a5b3966886ca7723e9e7/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