#!/bin/bash
### ---
### name: 'GERMLINE_CNV:ProcessBatch (1)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/sarek/altera_cnv:0.4.0'
### outputs:
### - 'counts_1.parquet'
### - 'sample_metrics_1.parquet'
### - 'ploidy_1.parquet'
### - 'B2377KTLT3_1__sex_calls.parquet'
### - 'B2377KTLT3_1__sex_calls.png'
### ...
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/43/8940e298004d5cefac289b95ebb498/.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 1029_IBG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3LL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_XV9-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3OP-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_0IB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BH0W-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_48U-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1047_OV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_2FV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_41Q-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_41F-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1047_NZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1047_ES-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BM6G-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_G4G-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_02C-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_IEQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_43J-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BLTU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BEFS-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_0YX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_HRY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_D1M-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_YXZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_HK0-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_FYQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_L86-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_15R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1047_B6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_47P-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_2JW-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1047_HC-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3MW-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BC0-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_29M-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BCKB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3OJ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_G9R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_WPT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_XIG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_BOVO-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3Q4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_UMV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f altera_v3_variable_regions.bed
rm -f .command.run
rm -f germline_cnv_input.csv
rm -f 1136_3PX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_153-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_01F-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_48S-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_DGN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f altera_v3_panel.bed
rm -f 1136_234-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_C4V-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_DK8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_DPZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_2M6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_16D-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f .command.sh
rm -f 1136_3BQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3Y6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_367-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_ILF-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_0IY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_2P4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3E1-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3WN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_0C8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_2RU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_21Y-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1136_3Z6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_ZJT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
rm -f 1029_G60-N1-BDNA-1_B23KFG5LT4_1_counts.tsv
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7ad8285ec0d5f6e3e135731e0f2145/1029_IBG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_IBG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/9b9a4b03575a323ca568b8dfdc3f0c/1136_3LL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3LL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/224b8d9d25370df392fd8e3eff9595/1029_XV9-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_XV9-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/cd02745d0820a93ff7ea1dff253ee5/1136_3OP-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3OP-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/95abd46d71043b39d25c6b0d3e58a0/1136_0IB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_0IB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/51c1b68ff87d5de90d1794beae6fc0/1029_BH0W-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BH0W-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/12f6bc221b46791f3d23742af18248/1136_48U-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_48U-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/9c802c3cc6519e60e4a1d3af0c0f8d/1047_OV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1047_OV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/efa71b2b545933e13eb86ff388b84f/1136_2FV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_2FV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/71305694dd3cae07a1f4289ebc9afe/1136_41Q-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_41Q-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/8b0502fd00131e3eb8b2ba1d8907e8/1136_41F-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_41F-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/042e4369f83093098460a5558721bf/1047_NZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1047_NZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/4a7ceb1ef2004e96d47e7e7b3c0c33/1047_ES-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1047_ES-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/65122e37f41421aac699fbdd035f7f/1029_BM6G-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BM6G-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/a03191c19c6040b64a1a320937e9dc/1029_G4G-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_G4G-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/40b9b199c66011653daad7246bfcf8/1136_02C-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_02C-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/1316c28938ed9fa45cede14d41aa8e/1029_IEQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_IEQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/911bb27d667aacfe014566504d02b6/1136_43J-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_43J-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/e0a4c66c90a1925df54a7da053a260/1029_BLTU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BLTU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/a5991359c544b315a8c4f75c8231ac/1029_BEFS-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BEFS-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/730540703f848f5628ae71d3cce57f/1136_0YX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_0YX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/c08da8a51e2ec29b62ff5b44028d45/1029_HRY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_HRY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/3e0d100ded10c3993262691d26fffd/1029_D1M-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_D1M-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/fe3a38b485dce8a3130dd4a9e7e595/1029_YXZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_YXZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/ddae959fba22e0f06474b32ed050cc/1029_HK0-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_HK0-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/0eb6ad85000c95824278231fe270f0/1029_FYQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_FYQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/0d411242817be1f350294ff7e01c29/1029_L86-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_L86-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/1399c42b4d2a95fea976c6a8e07a82/1136_15R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_15R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/e87001d32dc59bb738555d1b4fd0ab/1047_B6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1047_B6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/2957906578c0bd8e60d4942ef8e45d/1136_47P-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_47P-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/adb574f366ceab01bfe991e03c2d80/1136_2JW-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_2JW-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/d46e46c662554ddda7c38409719861/1047_HC-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1047_HC-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/ba3f1888774a8443421d4e901fd732/1136_3MW-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3MW-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/9a59a5e0e42ed64b94088433ad85f4/1029_BC0-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BC0-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/5250fe4b2c6499cb186349ecda51b5/1136_29M-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_29M-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/0ed1479036b78aa6cbf90089fe6420/1029_BCKB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BCKB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/b14c93790643ebd07e7e56df6201dd/1136_3OJ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3OJ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/7903305e3387a33349363529b10300/1029_G9R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_G9R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/446e6edc53cdc33f06167ae7ec251e/1029_BKVL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BKVL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/8c8cb36717989a4ebf571f5c9e0554/1029_WPT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_WPT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/4f288ff0d7864975a67728d1da6af2/1029_XIG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_XIG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/05b6e011662c68a8c56830ee2be463/1029_BOVO-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_BOVO-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/d380d124b8e297b37c8b6ff6c11f5b/1136_3Q4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3Q4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/e9fb84040694b9ab0e6a5261ac8ec4/1029_UMV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_UMV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/efd076651d88b387ccc9db955c84e8/1029_HJ2-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_HJ2-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-platform-sandbox/platform_projects/altera_cnv/altera_v3_variable_regions.bed altera_v3_variable_regions.bed")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/cd/9a7cb8ec1737ac603960c5984a431a/germline_cnv_input.csv germline_cnv_input.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/b4a2ed8cafb5f5d720d602dca46121/1136_3PX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3PX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/d3e1f51a4babf080c922eb89185204/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/bb611b46681bdffde3cb21ac43ebaf/1136_153-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_153-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/4967e645c11336612e1716eb747088/1029_01F-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_01F-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/c5bd771c9be6e8ae2bc4aff9ebde7e/1136_48S-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_48S-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/b6504d40437515cde2d328114b0819/1029_DGN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_DGN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-platform-sandbox/platform_projects/altera_cnv/altera_v3_panel.bed altera_v3_panel.bed")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/9dc3def884d5d1199dd5719aabafd7/1136_234-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_234-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/60d969f8e5c5c9b9f447a294783fc1/1029_C4V-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_C4V-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/e27c58065c1cc0af15ff13f199bb2b/1029_DK8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_DK8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/c3602724cec35e6cc0c5d4c4715021/1029_DPZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_DPZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/bd372e951387c64372d71430833f1d/1136_2M6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_2M6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/b4d2ec7e4863744b186350db077a3a/1136_16D-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_16D-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/ee5e23e4b930cfd4c528ce1aac3b8c/1136_3BQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3BQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/16ce13d76f754e4ff1876dea38363e/1136_3Y6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3Y6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/f78db597e6aabf895a9105cc3ab317/1136_367-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_367-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/32d926dce18a1ed2ae498653a206a1/1029_ILF-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_ILF-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/ce7250112b179fa2eecf68b85e9c00/1136_0IY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_0IY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/a62ea3619f1365f6e9875940f15cb4/1136_2P4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_2P4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/dfab77bf6e64e97f133cceae9885f3/1136_3E1-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3E1-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/bc0bc05ed3e7a21b87e68dd1d69686/1136_3WN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3WN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/d48dda5319da32ac4b1477dcbf015c/1136_0C8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_0C8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/3290ae5dcfe075faf90c316a8d1195/1029_QZ1-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/c396168fa4848006870abf7e714731/1136_2RU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_2RU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/9472cdd442a4db5da615baa4cc9612/1136_21Y-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_21Y-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/80cbb9de717c89c2d91945c71c1df1/1136_3Z6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_3Z6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6fc984a9c03f04533fb390c91b4927/1029_ZJT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_ZJT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/df8baacd72f04d2287e06eb0faf82e/1029_G60-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1029_G60-N1-BDNA-1_B23KFG5LT4_1_counts.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (77 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d counts_1.parquet sample_metrics_1.parquet ploidy_1.parquet B2377KTLT3_1__sex_calls.parquet B2377KTLT3_1__sex_calls.png" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/8940e298004d5cefac289b95ebb498 || 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/43/8940e298004d5cefac289b95ebb498/.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