#!/bin/bash
### ---
### name: 'CNV_PIPE:CombineSummaries (FC13_cnv_mosaic_combine_summaries)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/bding/cnv_pipe:bding_1.0.6'
### outputs:
### - 'cnv_call_summary.tsv'
### - 'cnv_gene_summary.tsv'
### ...
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/fb/367264360b6efcb97ea003ab8e2851/.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)
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/c844b46c862b72a4e615f8578a225d/vcfs/cnv_call_471141418_r13.tsv call_summaries/cnv_call_471141418_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/ed53c1da51eb4f9607f82408d0af8c/vcfs/cnv_call_3700651506_r13.tsv call_summaries/cnv_call_3700651506_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/0687d276bda89f7aa622d6c9b29a66/vcfs/cnv_call_3700651382_r13.tsv call_summaries/cnv_call_3700651382_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/ef3ec54dc29e59d7aa62503616c0a1/vcfs/cnv_gene_3700663145_r13.tsv gene_summaries/cnv_gene_3700663145_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/ff8edfb737dafcd8447df6032daac6/vcfs/cnv_call_3700650997_r13.tsv call_summaries/cnv_call_3700650997_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/56d162d181280e0549e0c42cd9611f/vcfs/cnv_gene_3700663222_r13.tsv gene_summaries/cnv_gene_3700663222_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/044fefddd86bfa99e0986c95ab8566/vcfs/cnv_call_3700652049_r13.tsv call_summaries/cnv_call_3700652049_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/6d617ed8297e82a27405dd22176be5/vcfs/cnv_gene_3700651324_r13.tsv gene_summaries/cnv_gene_3700651324_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/e8a85f22edf477b69ad37d460c81d4/vcfs/cnv_call_471141763_r13.tsv call_summaries/cnv_call_471141763_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/599776a5023fa35b40006f40c60df2/vcfs/cnv_gene_3700648970_r13.tsv gene_summaries/cnv_gene_3700648970_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/b25d324c68490e2aee8c8bb283be84/vcfs/cnv_call_3700652017_r13.tsv call_summaries/cnv_call_3700652017_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/575263bfbee7298c6cfa24954a2bf1/vcfs/cnv_gene_3574103386_r13.tsv gene_summaries/cnv_gene_3574103386_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/8b7d0ac6b866d66be2f4907da37516/vcfs/cnv_gene_3700651433_r13.tsv gene_summaries/cnv_gene_3700651433_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/0262cd115ac196a484f28a626203ec/vcfs/cnv_call_471141748_r13.tsv call_summaries/cnv_call_471141748_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/5da31ec171d88507307c7f04d1535c/vcfs/cnv_gene_3700663239_r13.tsv gene_summaries/cnv_gene_3700663239_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/9ba14f1a210e22b35d74e9969bdf61/vcfs/cnv_call_3700663153_r13.tsv call_summaries/cnv_call_3700663153_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/a333b5ba20cbd2aa39827ffb510d7b/vcfs/cnv_gene_3700650972_r13.tsv gene_summaries/cnv_gene_3700650972_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/54f028fd00adb076a6974a0cde4425/vcfs/cnv_gene_3700651510_r13.tsv gene_summaries/cnv_gene_3700651510_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/8a652cef97cfe42b73fa633c6d7b8c/vcfs/cnv_gene_3700648969_r13.tsv gene_summaries/cnv_gene_3700648969_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/01e779affcc442872936eefa5c17ae/vcfs/cnv_gene_471140782_r13.tsv gene_summaries/cnv_gene_471140782_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/e776cc5a9426cea260fb974fcb6739/vcfs/cnv_gene_471142226_r13.tsv gene_summaries/cnv_gene_471142226_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/54abe80851fe448ba59a159ee32abb/vcfs/cnv_call_3700652141_r13.tsv call_summaries/cnv_call_3700652141_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/a7f7fddf208e74a34a189ec1c6a2a5/vcfs/cnv_gene_3700663534_r13.tsv gene_summaries/cnv_gene_3700663534_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/4e1e89e14bdddcd11fed5559768e8a/vcfs/cnv_gene_3700650986_r13.tsv gene_summaries/cnv_gene_3700650986_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/5549db563cab48155d4551ba906843/vcfs/cnv_call_3700663592_r13.tsv call_summaries/cnv_call_3700663592_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/65ce368a1eedb28e07a8ee7efc0925/vcfs/cnv_gene_3700648890_r13.tsv gene_summaries/cnv_gene_3700648890_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/e189584a26c9ab25a6a685264e9c43/vcfs/cnv_call_3700663401_r13.tsv call_summaries/cnv_call_3700663401_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/5db7eab317e36f1424525ba269c37d/vcfs/cnv_call_3700651503_r13.tsv call_summaries/cnv_call_3700651503_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/b9a38c5421e4fd38bd8770d4059aba/vcfs/cnv_call_3700650994_r13.tsv call_summaries/cnv_call_3700650994_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/1eab68dfffc89aa8eb9cb36fdf8a52/vcfs/cnv_gene_3619659359_r13.tsv gene_summaries/cnv_gene_3619659359_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/0ec70a09dc7bf4e996dd2ab9361cec/vcfs/cnv_gene_3700663611_r13.tsv gene_summaries/cnv_gene_3700663611_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/d42e3d3cba88201418fe5b53f0a748/vcfs/cnv_gene_3700651029_r13.tsv gene_summaries/cnv_gene_3700651029_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/e3eccf329703455a18d549d58fe3ea/vcfs/cnv_gene_3700663428_r13.tsv gene_summaries/cnv_gene_3700663428_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/6ea3ab280e530b80f2e1280fa4f78c/vcfs/cnv_gene_3700652042_r13.tsv gene_summaries/cnv_gene_3700652042_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/759c2661d986454f52ce4aca04024e/vcfs/cnv_call_3700663374_r13.tsv call_summaries/cnv_call_3700663374_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/7f2fae02c1538f3c1c5676c40267a2/vcfs/cnv_gene_3700663584_r13.tsv gene_summaries/cnv_gene_3700663584_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/c8eb4c83d77c252af71321bfb18e5a/vcfs/cnv_call_3700652014_r13.tsv call_summaries/cnv_call_3700652014_r13.tsv")
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downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/3c96ea1c49d1fc5bd22096c6d448ea/vcfs/cnv_call_471141429_r13.tsv call_summaries/cnv_call_471141429_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/8cae304d82d41149eed0a11af048ca/vcfs/cnv_gene_3700663224_r13.tsv gene_summaries/cnv_gene_3700663224_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/f7d58ce300078d6158180a2d7c6139/vcfs/cnv_gene_3700651448_r13.tsv gene_summaries/cnv_gene_3700651448_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/32b46891b7a576115dd824391429aa/vcfs/cnv_call_3700663213_r13.tsv call_summaries/cnv_call_3700663213_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/ed53c1da51eb4f9607f82408d0af8c/vcfs/cnv_gene_3700651506_r13.tsv gene_summaries/cnv_gene_3700651506_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/78d50b50464c10c1b6876ad5b6d8d1/vcfs/cnv_call_3700652066_r13.tsv call_summaries/cnv_call_3700652066_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/8a652cef97cfe42b73fa633c6d7b8c/vcfs/cnv_call_3700648969_r13.tsv call_summaries/cnv_call_3700648969_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/68cde6e52fee568afd3ce387f2f01f/vcfs/cnv_gene_471203161_r13.tsv gene_summaries/cnv_gene_471203161_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/599776a5023fa35b40006f40c60df2/vcfs/cnv_call_3700648970_r13.tsv call_summaries/cnv_call_3700648970_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/49767e88b162bb953b901b4a3d01d4/vcfs/cnv_call_3700651040_r13.tsv call_summaries/cnv_call_3700651040_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/809db3524c1d0fe94076a96978e747/vcfs/cnv_call_3700663398_r13.tsv call_summaries/cnv_call_3700663398_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/14c57fcceaea7e7267754c32e69375/vcfs/cnv_call_3700663566_r13.tsv call_summaries/cnv_call_3700663566_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/4a4eb2460f064757388eb089cbdfaf/vcfs/cnv_call_3700650045_r13.tsv call_summaries/cnv_call_3700650045_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/2b2f7bf1cc3713df2316faa8cc349d/vcfs/cnv_call_3700663350_r13.tsv call_summaries/cnv_call_3700663350_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/e7ab1c3aff2247d34e635ca72392b0/vcfs/cnv_call_3700663367_r13.tsv call_summaries/cnv_call_3700663367_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/8bb6ac6440811223a1f4394288ea02/vcfs/cnv_gene_3700663560_r13.tsv gene_summaries/cnv_gene_3700663560_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/6be9060604381f4a4b6d5beafb0f56/vcfs/cnv_call_471141746_r13.tsv call_summaries/cnv_call_471141746_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/091b8274871937ab445f27c982bdbd/vcfs/cnv_gene_3700663361_r13.tsv gene_summaries/cnv_gene_3700663361_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/93dcd891c92d1ccfb343cb6627ba9e/vcfs/cnv_call_3700663597_r13.tsv call_summaries/cnv_call_3700663597_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/c9284f3cba3bb50de9d169b04e367b/vcfs/cnv_call_3700650033_r13.tsv call_summaries/cnv_call_3700650033_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/8e06c28390c53e4b3f354e402770f0/vcfs/cnv_gene_3700651313_r13.tsv gene_summaries/cnv_gene_3700651313_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/c84e70401cc59e9c5dab818ed0db8e/vcfs/cnv_gene_3700651008_r13.tsv gene_summaries/cnv_gene_3700651008_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d59e9d98979c2a200c9c7232d84012/vcfs/cnv_call_471142219_r13.tsv call_summaries/cnv_call_471142219_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/182dc52c677005017599bde04e6442/vcfs/cnv_call_3700651493_r13.tsv call_summaries/cnv_call_3700651493_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/ff713394e4f77f4086af7efdcd67a7/vcfs/cnv_gene_3700652023_r13.tsv gene_summaries/cnv_gene_3700652023_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/d530c02f2a16551c94a51cc0487340/vcfs/cnv_gene_3700651332_r13.tsv gene_summaries/cnv_gene_3700651332_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/7275cab98e1fbf54d93e0f466b27b9/vcfs/cnv_gene_3700663373_r13.tsv gene_summaries/cnv_gene_3700663373_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/4a2d1d0ef279a82a07e866514a7951/vcfs/cnv_gene_3700663400_r13.tsv gene_summaries/cnv_gene_3700663400_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/a7aff294f647cd2321976bc71e3fa5/vcfs/cnv_call_3574260751_r13.tsv call_summaries/cnv_call_3574260751_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/8a1fa473743898f2847e10de5834c1/vcfs/cnv_call_3700651474_r13.tsv call_summaries/cnv_call_3700651474_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/c2bc756d0f35b30c5dc0d5a9f3a17d/vcfs/cnv_call_3619658675_r13.tsv call_summaries/cnv_call_3619658675_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/d3480d4df4094f4f5d4f730c8e861a/vcfs/cnv_call_471141430_r13.tsv call_summaries/cnv_call_471141430_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/3add1d4377c8f9fa9b80086046a16f/vcfs/cnv_gene_3619659347_r13.tsv gene_summaries/cnv_gene_3619659347_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/5936acfefde62ad146544d7a6c3058/vcfs/cnv_gene_3700663206_r13.tsv gene_summaries/cnv_gene_3700663206_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/e2949656ea183f155beec70f7d3edc/vcfs/cnv_call_3700651034_r13.tsv call_summaries/cnv_call_3700651034_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/c27b420ff867794335744e99aa7afd/vcfs/cnv_gene_3700651015_r13.tsv gene_summaries/cnv_gene_3700651015_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/6ea3ab280e530b80f2e1280fa4f78c/vcfs/cnv_call_3700652042_r13.tsv call_summaries/cnv_call_3700652042_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/44df604a3a8677e9c39d2055c7fc8d/vcfs/cnv_call_3700652072_r13.tsv call_summaries/cnv_call_3700652072_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/2d278b5412a1f29ab695d972daee21/vcfs/cnv_gene_3700652089_r13.tsv gene_summaries/cnv_gene_3700652089_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/be5b655f8ce921fecb2cee852c7007/vcfs/cnv_call_3700651432_r13.tsv call_summaries/cnv_call_3700651432_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/6e509148df9b1705937c6ab098779a/vcfs/cnv_call_3700652078_r13.tsv call_summaries/cnv_call_3700652078_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/5e87bb1b2794eb7ef0e9ea735cbda1/vcfs/cnv_gene_3700652104_r13.tsv gene_summaries/cnv_gene_3700652104_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/04adcd29339a26e663404e02d81711/vcfs/cnv_call_3700663349_r13.tsv call_summaries/cnv_call_3700663349_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/e646495f28b7bd484f7200e5ca034f/vcfs/cnv_call_3700648921_r13.tsv call_summaries/cnv_call_3700648921_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/e776cc5a9426cea260fb974fcb6739/vcfs/cnv_call_471142226_r13.tsv call_summaries/cnv_call_471142226_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/79bfb93274419318b38a8e62356756/vcfs/cnv_gene_3700663559_r13.tsv gene_summaries/cnv_gene_3700663559_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/4c9e132a3deb5d3978f7eb7af8543c/vcfs/cnv_call_471141764_r13.tsv call_summaries/cnv_call_471141764_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/e363c33bcc269563213c90029d1cdb/vcfs/cnv_call_3700650063_r13.tsv call_summaries/cnv_call_3700650063_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/43f9442bef5cfbbe71f31386165428/vcfs/cnv_call_471142232_r13.tsv call_summaries/cnv_call_471142232_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/2091333a84772bc38a1ba92f00fbbc/vcfs/cnv_call_3700651314_r13.tsv call_summaries/cnv_call_3700651314_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/83bff20cad0dc1eda78c6838d38134/vcfs/cnv_call_471203140_r13.tsv call_summaries/cnv_call_471203140_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/da0850f103068ef6e3eec483926207/vcfs/cnv_gene_3700663405_r13.tsv gene_summaries/cnv_gene_3700663405_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/eb553269e6ad9025c73092029e25e6/vcfs/cnv_gene_3700651480_r13.tsv gene_summaries/cnv_gene_3700651480_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/a626d776b6b268f206f7b45aa45b72/vcfs/cnv_gene_471140791_r13.tsv gene_summaries/cnv_gene_471140791_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/305f570c88afc239861eee44a87336/vcfs/cnv_gene_3700651325_r13.tsv gene_summaries/cnv_gene_3700651325_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/1c7458be0e8f0eb49680c75ba4aea7/vcfs/cnv_gene_3700663604_r13.tsv gene_summaries/cnv_gene_3700663604_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/11386a85cb40a41e0bd3bf26066643/vcfs/cnv_call_3700650976_r13.tsv call_summaries/cnv_call_3700650976_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/7e84ff529bbbe3e0860332f520be68/vcfs/cnv_call_3700663337_r13.tsv call_summaries/cnv_call_3700663337_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/b0429a68fee44ff7aafa7c09629e73/vcfs/cnv_call_471140793_r13.tsv call_summaries/cnv_call_471140793_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/518f192a21dd38bcbd28ae2ac01418/vcfs/cnv_call_3700663536_r13.tsv call_summaries/cnv_call_3700663536_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/80c8baa1a51629119a51f3608505fc/vcfs/cnv_gene_471201190_2_r13.tsv gene_summaries/cnv_gene_471201190_2_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/59855d142e35d348be31a11dedb1f1/vcfs/cnv_gene_3601213931_r13.tsv gene_summaries/cnv_gene_3601213931_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/4895661cbc0eb2e5da9934bf845943/vcfs/cnv_call_3700652096_r13.tsv call_summaries/cnv_call_3700652096_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/6522aa597f86841dc0d3525e8f6760/vcfs/cnv_call_3700663232_r13.tsv call_summaries/cnv_call_3700663232_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/b701ddb3cee4d82e0d070456168c33/vcfs/cnv_gene_3700663590_r13.tsv gene_summaries/cnv_gene_3700663590_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/197fdbe26bc76544b512dea3cf2042/vcfs/cnv_gene_3700663391_r13.tsv gene_summaries/cnv_gene_3700663391_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/9b863df589a36cef7aa284a25a0ec8/vcfs/cnv_call_3700663181_r13.tsv call_summaries/cnv_call_3700663181_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/fdb27af6c31ba1ff7df2e4b93519c2/vcfs/cnv_call_3579447764_r13.tsv call_summaries/cnv_call_3579447764_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/5db728227f7671fb9fe2908809f061/vcfs/cnv_call_3619658687_r13.tsv call_summaries/cnv_call_3619658687_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/a235f7905299f4ffdb185c0e7baf36/vcfs/cnv_call_3700663431_r13.tsv call_summaries/cnv_call_3700663431_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/d157700a735b4178aae25d6b423040/vcfs/cnv_call_3700663392_r13.tsv call_summaries/cnv_call_3700663392_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/b112d5bb31bbb97d9b6fa265ba503d/vcfs/cnv_call_471140781_r13.tsv call_summaries/cnv_call_471140781_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/4ecb347093269653f70d7fb3c4ccf8/vcfs/cnv_call_3700651456_r13.tsv call_summaries/cnv_call_3700651456_r13.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/c25af69fda5f4704fb53023911223f/vcfs/cnv_call_3700663220_r13.tsv call_summaries/cnv_call_3700663220_r13.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (744 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d cnv_call_summary.tsv cnv_gene_summary.tsv" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/367264360b6efcb97ea003ab8e2851")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/367264360b6efcb97ea003ab8e2851 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/367264360b6efcb97ea003ab8e2851 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/367264360b6efcb97ea003ab8e2851 || 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/fb/367264360b6efcb97ea003ab8e2851/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/77/b617ba5f7efa5a8f2d01756257fc85/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