#!/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'
### - 'A237YLNLT3_1__sex_calls.parquet'
### - 'A237YLNLT3_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/b2/655a5e8e00442492d221f5536ab6cf/.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_BJH0-N1-BDNA-1_2375WFLT3_s35_counts.tsv
rm -f 1029_GGQ-N1-BDNA-1_2375WFLT3_s70_counts.tsv
rm -f 1029_4Z2-N1-BDNA-1_2375WFLT3_s12_counts.tsv
rm -f 1029_BGFD-N1-BDNA-1_2375WFLT3_s30_counts.tsv
rm -f 1029_8BO-N1-BDNA-1_2375WFLT3_s18_counts.tsv
rm -f 1029_BA0-N2-BDNA-1_2375WFLT3_s20_counts.tsv
rm -f 1029_3N0-N1-BDNA-1_2375WFLT3_s09_counts.tsv
rm -f 1029_BS78-N1-BDNA-1_2375WFLT3_s51_counts.tsv
rm -f 1029_8OI-N1-BDNA-1_2375WFLT3_s19_counts.tsv
rm -f 1029_BOSD-N1-BDNA-1_2375WFLT3_s43_counts.tsv
rm -f 1029_BP21-N1-BDNA-1_2375WFLT3_s44_counts.tsv
rm -f 1029_EM-N1-BDNA-1_2375WFLT3_s61_counts.tsv
rm -f 1029_2LI-N1-BDNA-1_2375WFLT3_s08_counts.tsv
rm -f 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26_counts.tsv
rm -f 1029_BCTO-N1-BDNA-1_2375WFLT3_s25_counts.tsv
rm -f 1029_BQKE-N1-BDNA-1_2375WFLT3_s47_counts.tsv
rm -f 1029_0DT-N1-BDNA-1_2375WFLT3_s03_counts.tsv
rm -f 1029_BPLF-N1-BDNA-1_2375WFLT3_s45_counts.tsv
rm -f 1029_BF2U-N1-BDNA-1_2375WFLT3_s27_counts.tsv
rm -f 1029_05O-N1-BDNA-1_2375WFLT3_s02_counts.tsv
rm -f 1029_E36-N1-BDNA-1_2375WFLT3_s58_counts.tsv
rm -f 1029_4J3-N1-BDNA-1_2375WFLT3_s11_counts.tsv
rm -f 1029_5O3-N1-BDNA-1_2375WFLT3_s15_counts.tsv
rm -f 1029_FXQ-N1-BDNA-1_2375WFLT3_s67_counts.tsv
rm -f 1029_BSWE-N1-BDNA-1_2375WFLT3_s53_counts.tsv
rm -f 1029_EDH-N1-BDNA-1_2375WFLT3_s59_counts.tsv
rm -f 1029_FBB-N1-BDNA-1_2375WFLT3_s63_counts.tsv
rm -f 1029_EFW-N1-BDNA-1_2375WFLT3_s60_counts.tsv
rm -f 1029_BNG8-N1-BDNA-1_2375WFLT3_s40_counts.tsv
rm -f 1029_BSOQ-N1-BDNA-1_2375WFLT3_s52_counts.tsv
rm -f 1029_BQXQ-N1-BDNA-1_2375WFLT3_s49_counts.tsv
rm -f 1029_BK2H-N1-BDNA-1_2375WFLT3_s36_counts.tsv
rm -f 1029_BLU1-N1-BDNA-1_2375WFLT3_s38_counts.tsv
rm -f altera_v3_variable_regions.bed
rm -f .command.run
rm -f germline_cnv_input.csv
rm -f 1029_DV0-N1-BDNA-1_2375WFLT3_s57_counts.tsv
rm -f 1029_BFKM-N1-BDNA-1_2375WFLT3_s28_counts.tsv
rm -f 1029_BGMF-N1-BDNA-1_2375WFLT3_s31_counts.tsv
rm -f 1029_3OH-N1-BDNA-1_2375WFLT3_s10_counts.tsv
rm -f 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_counts.tsv
rm -f 1029_BSZ8-N1-BDNA-1_2375WFLT3_s54_counts.tsv
rm -f 1029_1G0-N1-BDNA-1_2375WFLT3_s05_counts.tsv
rm -f altera_v3_panel.bed
rm -f 1029_FWL-N1-BDNA-1_2375WFLT3_s66_counts.tsv
rm -f 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39_counts.tsv
rm -f 1029_BQD7-N1-BDNA-1_2375WFLT3_s46_counts.tsv
rm -f 1029_C35-N1-BDNA-1_2375WFLT3_s55_counts.tsv
rm -f 1029_DOC-N1-BDNA-1_2375WFLT3_s56_counts.tsv
rm -f .command.sh
rm -f 1029_FR4-N1-BDNA-1_2375WFLT3_s65_counts.tsv
rm -f 1029_G5I-N1-BDNA-1_2375WFLT3_s68_counts.tsv
rm -f 1029_2IN-N1-BDNA-1_2375WFLT3_s07_counts.tsv
rm -f 1029_BG5-N1-BDNA-1_2375WFLT3_s29_counts.tsv
rm -f 1029_EMM-N1-BDNA-1_2375WFLT3_s62_counts.tsv
rm -f 1029_BRTT-N1-BDNA-1_2375WFLT3_s50_counts.tsv
rm -f 1029_BIHC-N1-BDNA-1_2375WFLT3_s33_counts.tsv
rm -f 1029_BBS1-N1-BDNA-1_2375WFLT3_s23_counts.tsv
rm -f 1029_BIHO-N1-BDNA-1_2375WFLT3_s34_counts.tsv
rm -f 1029_G94-N1-BDNA-1_2375WFLT3_s69_counts.tsv
rm -f 1029_BBOC-N1-BDNA-1_2375WFLT3_s22_counts.tsv
rm -f 1029_BO4Y-N1-BDNA-1_2375WFLT3_s41_counts.tsv
rm -f 1029_GW0-N1-BDNA-1_2375WFLT3_s72_counts.tsv
rm -f 1029_BLH5-N1-BDNA-1_2375WFLT3_s37_counts.tsv
rm -f 1029_BOHJ-N1-BDNA-1_2375WFLT3_s42_counts.tsv
rm -f 1029_7Y1-N1-BDNA-1_2375WFLT3_s16_counts.tsv
rm -f 1029_GS7-N1-BDNA-1_2375WFLT3_s71_counts.tsv
rm -f 1029_032-N1-BDNA-1_2375WFLT3_s01_counts.tsv
rm -f 1029_56D-N1-BDNA-1_2375WFLT3_s13_counts.tsv
rm -f 1029_BQMQ-N1-BDNA-1_2375WFLT3_s48_counts.tsv
rm -f 1029_0NX-N1-BDNA-1_2375WFLT3_s04_counts.tsv
rm -f 1029_1H5-N1-BDNA-1_2375WFLT3_s06_counts.tsv
rm -f 1029_5IX-N1-BDNA-1_2375WFLT3_s14_counts.tsv
rm -f 1029_8AV-N1-BDNA-1_2375WFLT3_s17_counts.tsv
rm -f 1029_BCB6-N1-BDNA-1_2375WFLT3_s24_counts.tsv
rm -f 1029_BICA-N1-BDNA-1_2375WFLT3_s32_counts.tsv
rm -f 1029_FOO-N1-BDNA-1_2375WFLT3_s64_counts.tsv
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/56b17d3eb6374c13e884378d9ddb2b/1029_BJH0-N1-BDNA-1_2375WFLT3_s35_counts.tsv 1029_BJH0-N1-BDNA-1_2375WFLT3_s35_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/c07efce28cbe0f0c7702c60b309ef0/1029_GGQ-N1-BDNA-1_2375WFLT3_s70_counts.tsv 1029_GGQ-N1-BDNA-1_2375WFLT3_s70_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/79d2000f6f971e374de821188e54d0/1029_4Z2-N1-BDNA-1_2375WFLT3_s12_counts.tsv 1029_4Z2-N1-BDNA-1_2375WFLT3_s12_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/7725be6914c749c1779cf286874eb2/1029_BGFD-N1-BDNA-1_2375WFLT3_s30_counts.tsv 1029_BGFD-N1-BDNA-1_2375WFLT3_s30_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/e09996b4bb25d78e0b89850e36b9da/1029_8BO-N1-BDNA-1_2375WFLT3_s18_counts.tsv 1029_8BO-N1-BDNA-1_2375WFLT3_s18_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/31c618c30c5255c96a354706d847ea/1029_BA0-N2-BDNA-1_2375WFLT3_s20_counts.tsv 1029_BA0-N2-BDNA-1_2375WFLT3_s20_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/0837c34324bf08b948df2d266b9417/1029_3N0-N1-BDNA-1_2375WFLT3_s09_counts.tsv 1029_3N0-N1-BDNA-1_2375WFLT3_s09_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/b32fe70cf5d1bc8526d029a6de9162/1029_BS78-N1-BDNA-1_2375WFLT3_s51_counts.tsv 1029_BS78-N1-BDNA-1_2375WFLT3_s51_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/583f2ef7542a7d7b2e0e78c55001c1/1029_8OI-N1-BDNA-1_2375WFLT3_s19_counts.tsv 1029_8OI-N1-BDNA-1_2375WFLT3_s19_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/b4e3a9b25c1ff04288278006b40097/1029_BOSD-N1-BDNA-1_2375WFLT3_s43_counts.tsv 1029_BOSD-N1-BDNA-1_2375WFLT3_s43_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/3605885535b7438eb9d6b2bcbbf404/1029_BP21-N1-BDNA-1_2375WFLT3_s44_counts.tsv 1029_BP21-N1-BDNA-1_2375WFLT3_s44_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/336cc0fa266c6538f1075b50443782/1029_EM-N1-BDNA-1_2375WFLT3_s61_counts.tsv 1029_EM-N1-BDNA-1_2375WFLT3_s61_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/bc897108e05366ebc6f07260eda095/1029_2LI-N1-BDNA-1_2375WFLT3_s08_counts.tsv 1029_2LI-N1-BDNA-1_2375WFLT3_s08_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7e70b1ddddd6e68c600f7ec2e52e48/1029_BDOZ-N1-BDNA-1_2375WFLT3_s26_counts.tsv 1029_BDOZ-N1-BDNA-1_2375WFLT3_s26_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/3cc8cb174e03ba2298d1cbf81df1e2/1029_BCTO-N1-BDNA-1_2375WFLT3_s25_counts.tsv 1029_BCTO-N1-BDNA-1_2375WFLT3_s25_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/20c9401a0576f4fc63b9328ba1dd32/1029_BQKE-N1-BDNA-1_2375WFLT3_s47_counts.tsv 1029_BQKE-N1-BDNA-1_2375WFLT3_s47_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/b709e458ece9a8b0056c086fb7ad0e/1029_0DT-N1-BDNA-1_2375WFLT3_s03_counts.tsv 1029_0DT-N1-BDNA-1_2375WFLT3_s03_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/54acdf9a78bf129bbb1d1769c5d51e/1029_BPLF-N1-BDNA-1_2375WFLT3_s45_counts.tsv 1029_BPLF-N1-BDNA-1_2375WFLT3_s45_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/5e7bd6b0f1647bc0a09a06acdba42e/1029_BF2U-N1-BDNA-1_2375WFLT3_s27_counts.tsv 1029_BF2U-N1-BDNA-1_2375WFLT3_s27_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c53c35fda12d4e6a0204b03833fc64/1029_05O-N1-BDNA-1_2375WFLT3_s02_counts.tsv 1029_05O-N1-BDNA-1_2375WFLT3_s02_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/b9522ac1b128fe18c19160c2db30ef/1029_E36-N1-BDNA-1_2375WFLT3_s58_counts.tsv 1029_E36-N1-BDNA-1_2375WFLT3_s58_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/964c299bb92e6041985b2400d9876e/1029_4J3-N1-BDNA-1_2375WFLT3_s11_counts.tsv 1029_4J3-N1-BDNA-1_2375WFLT3_s11_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/463c408563588283e7289bf2a553f1/1029_5O3-N1-BDNA-1_2375WFLT3_s15_counts.tsv 1029_5O3-N1-BDNA-1_2375WFLT3_s15_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/95249640d2fb02fa0fabd8c6058573/1029_FXQ-N1-BDNA-1_2375WFLT3_s67_counts.tsv 1029_FXQ-N1-BDNA-1_2375WFLT3_s67_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/e114e25b995704351da98eddd17cce/1029_BSWE-N1-BDNA-1_2375WFLT3_s53_counts.tsv 1029_BSWE-N1-BDNA-1_2375WFLT3_s53_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/cb13cb4d1fb030774512b6541d84f4/1029_EDH-N1-BDNA-1_2375WFLT3_s59_counts.tsv 1029_EDH-N1-BDNA-1_2375WFLT3_s59_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/dffce4f9e04b149a5621c26d3a2fe5/1029_FBB-N1-BDNA-1_2375WFLT3_s63_counts.tsv 1029_FBB-N1-BDNA-1_2375WFLT3_s63_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/557d0608c8367d04d93526856ecee0/1029_EFW-N1-BDNA-1_2375WFLT3_s60_counts.tsv 1029_EFW-N1-BDNA-1_2375WFLT3_s60_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/956716b241866ac04f4361dbb7e73f/1029_BNG8-N1-BDNA-1_2375WFLT3_s40_counts.tsv 1029_BNG8-N1-BDNA-1_2375WFLT3_s40_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/6f47f3d788cb6f3c506a182b69b985/1029_BSOQ-N1-BDNA-1_2375WFLT3_s52_counts.tsv 1029_BSOQ-N1-BDNA-1_2375WFLT3_s52_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/1f57a011843311f5f0665b87a194f0/1029_BQXQ-N1-BDNA-1_2375WFLT3_s49_counts.tsv 1029_BQXQ-N1-BDNA-1_2375WFLT3_s49_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/c3f21c6e1a018a58157fb17c86104e/1029_BK2H-N1-BDNA-1_2375WFLT3_s36_counts.tsv 1029_BK2H-N1-BDNA-1_2375WFLT3_s36_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/ee44550c4f5804e79fd0aee7bc8996/1029_BLU1-N1-BDNA-1_2375WFLT3_s38_counts.tsv 1029_BLU1-N1-BDNA-1_2375WFLT3_s38_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/b2/655a5e8e00442492d221f5536ab6cf/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/70/007dda07feb59db4b8ac943f218d82/germline_cnv_input.csv germline_cnv_input.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/d40722da8329eca64e91f387d5c4ec/1029_DV0-N1-BDNA-1_2375WFLT3_s57_counts.tsv 1029_DV0-N1-BDNA-1_2375WFLT3_s57_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/1a8dd75a0fd6cb0be2b72b55e68431/1029_BFKM-N1-BDNA-1_2375WFLT3_s28_counts.tsv 1029_BFKM-N1-BDNA-1_2375WFLT3_s28_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ae700208cf985bf483effc62025e53/1029_BGMF-N1-BDNA-1_2375WFLT3_s31_counts.tsv 1029_BGMF-N1-BDNA-1_2375WFLT3_s31_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/b67d8a15418624ce036e2b74eac12c/1029_3OH-N1-BDNA-1_2375WFLT3_s10_counts.tsv 1029_3OH-N1-BDNA-1_2375WFLT3_s10_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/c5bc00f401db8abc1bd896a77eacc4/1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_counts.tsv 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/d16bd788dadf2743c091ffd3e30bf6/1029_BSZ8-N1-BDNA-1_2375WFLT3_s54_counts.tsv 1029_BSZ8-N1-BDNA-1_2375WFLT3_s54_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/e17989ff9342beb95916a5b1ab1899/1029_1G0-N1-BDNA-1_2375WFLT3_s05_counts.tsv 1029_1G0-N1-BDNA-1_2375WFLT3_s05_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/41/51517c02f14f3ee49520a051b16827/1029_FWL-N1-BDNA-1_2375WFLT3_s66_counts.tsv 1029_FWL-N1-BDNA-1_2375WFLT3_s66_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/3332d7b10d6644659625a17309cf86/1029_BN9Y-N1-BDNA-1_2375WFLT3_s39_counts.tsv 1029_BN9Y-N1-BDNA-1_2375WFLT3_s39_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/118c5d25bbf2fb9fcddba415f73fbe/1029_BQD7-N1-BDNA-1_2375WFLT3_s46_counts.tsv 1029_BQD7-N1-BDNA-1_2375WFLT3_s46_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/17d61a8c6366cb3c66d1b49f398d2a/1029_C35-N1-BDNA-1_2375WFLT3_s55_counts.tsv 1029_C35-N1-BDNA-1_2375WFLT3_s55_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/9c27f2b85dd48bb8c5a3fd8ce1260b/1029_DOC-N1-BDNA-1_2375WFLT3_s56_counts.tsv 1029_DOC-N1-BDNA-1_2375WFLT3_s56_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/f4058eea8b5e3ec1d930d9f4db6015/1029_FR4-N1-BDNA-1_2375WFLT3_s65_counts.tsv 1029_FR4-N1-BDNA-1_2375WFLT3_s65_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/c6060c7c103e0369bc862ace1ae5ed/1029_G5I-N1-BDNA-1_2375WFLT3_s68_counts.tsv 1029_G5I-N1-BDNA-1_2375WFLT3_s68_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/c731a5fdc12a2841b7c55392f655e1/1029_2IN-N1-BDNA-1_2375WFLT3_s07_counts.tsv 1029_2IN-N1-BDNA-1_2375WFLT3_s07_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/9c117a589bcf3e07650fc61677eec2/1029_BG5-N1-BDNA-1_2375WFLT3_s29_counts.tsv 1029_BG5-N1-BDNA-1_2375WFLT3_s29_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/254f6e2b654fc81c5efe9675682b45/1029_EMM-N1-BDNA-1_2375WFLT3_s62_counts.tsv 1029_EMM-N1-BDNA-1_2375WFLT3_s62_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/e08a9cfbdef4848f10b11b3b1ee413/1029_BRTT-N1-BDNA-1_2375WFLT3_s50_counts.tsv 1029_BRTT-N1-BDNA-1_2375WFLT3_s50_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/3457bfd3161d8b5d0e124aaa4f63f6/1029_BIHC-N1-BDNA-1_2375WFLT3_s33_counts.tsv 1029_BIHC-N1-BDNA-1_2375WFLT3_s33_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/140449366c3b9f54f91c79a77930f5/1029_BBS1-N1-BDNA-1_2375WFLT3_s23_counts.tsv 1029_BBS1-N1-BDNA-1_2375WFLT3_s23_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0cb7afefd0ce22d651b0539e9ea3c8/1029_BIHO-N1-BDNA-1_2375WFLT3_s34_counts.tsv 1029_BIHO-N1-BDNA-1_2375WFLT3_s34_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/82b417fb75d1860bc3b5b88eba9319/1029_G94-N1-BDNA-1_2375WFLT3_s69_counts.tsv 1029_G94-N1-BDNA-1_2375WFLT3_s69_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/e288c27a492ca3ed94a9a811d12826/1029_BBOC-N1-BDNA-1_2375WFLT3_s22_counts.tsv 1029_BBOC-N1-BDNA-1_2375WFLT3_s22_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/764b7c4e2f3ae0b918cd1324cdbd90/1029_BO4Y-N1-BDNA-1_2375WFLT3_s41_counts.tsv 1029_BO4Y-N1-BDNA-1_2375WFLT3_s41_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/5f8bbd3bd45c9346f2e7d4bc411a4c/1029_GW0-N1-BDNA-1_2375WFLT3_s72_counts.tsv 1029_GW0-N1-BDNA-1_2375WFLT3_s72_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/36cc0fdb29d4b388ea382f19018482/1029_BLH5-N1-BDNA-1_2375WFLT3_s37_counts.tsv 1029_BLH5-N1-BDNA-1_2375WFLT3_s37_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/9d7435ce361e54b639427980374eb9/1029_BOHJ-N1-BDNA-1_2375WFLT3_s42_counts.tsv 1029_BOHJ-N1-BDNA-1_2375WFLT3_s42_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/1615443e029cc7bf3b7aa633a1ec61/1029_7Y1-N1-BDNA-1_2375WFLT3_s16_counts.tsv 1029_7Y1-N1-BDNA-1_2375WFLT3_s16_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/2a38ad76b4d345a5348bb24d43d11c/1029_GS7-N1-BDNA-1_2375WFLT3_s71_counts.tsv 1029_GS7-N1-BDNA-1_2375WFLT3_s71_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/18d8bba8b8b481bb97912832b514e1/1029_032-N1-BDNA-1_2375WFLT3_s01_counts.tsv 1029_032-N1-BDNA-1_2375WFLT3_s01_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/1b558a45b3dc0f695e74c42fadba35/1029_56D-N1-BDNA-1_2375WFLT3_s13_counts.tsv 1029_56D-N1-BDNA-1_2375WFLT3_s13_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/940850aee002ac1e1ed078c1c8c118/1029_BQMQ-N1-BDNA-1_2375WFLT3_s48_counts.tsv 1029_BQMQ-N1-BDNA-1_2375WFLT3_s48_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/5e8678d5505bd8904062497f480285/1029_0NX-N1-BDNA-1_2375WFLT3_s04_counts.tsv 1029_0NX-N1-BDNA-1_2375WFLT3_s04_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/4f6b148dd98e18d50575ffa2359f69/1029_1H5-N1-BDNA-1_2375WFLT3_s06_counts.tsv 1029_1H5-N1-BDNA-1_2375WFLT3_s06_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/2cd66476e9a6842b6951e104d0a6ca/1029_5IX-N1-BDNA-1_2375WFLT3_s14_counts.tsv 1029_5IX-N1-BDNA-1_2375WFLT3_s14_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/796b57c10ab63a6f66a72b1a126a02/1029_8AV-N1-BDNA-1_2375WFLT3_s17_counts.tsv 1029_8AV-N1-BDNA-1_2375WFLT3_s17_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f32592b4122d41acd2d8e4ff341aa2/1029_BCB6-N1-BDNA-1_2375WFLT3_s24_counts.tsv 1029_BCB6-N1-BDNA-1_2375WFLT3_s24_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/b2ee528d8be17ad1eb8b0479a19b85/1029_BICA-N1-BDNA-1_2375WFLT3_s32_counts.tsv 1029_BICA-N1-BDNA-1_2375WFLT3_s32_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/f9429bcb25dab14b7537a1110303f7/1029_FOO-N1-BDNA-1_2375WFLT3_s64_counts.tsv 1029_FOO-N1-BDNA-1_2375WFLT3_s64_counts.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (77 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d counts_1.parquet sample_metrics_1.parquet ploidy_1.parquet A237YLNLT3_1__sex_calls.parquet A237YLNLT3_1__sex_calls.png" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf || 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/b2/655a5e8e00442492d221f5536ab6cf/.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