#!/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'
### - 'B23H3Y2LT3_1__sex_calls.parquet'
### - 'B23H3Y2LT3_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/3b/5fb84b9b25028695977080974e1a0c/.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_XI2-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_7WX-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7LD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_2QY-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1029_YCN-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_883-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7MF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_80B-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f NA12878_c_0002_gDNA_0006_A23NMNVLT4_1_counts.tsv
rm -f 1136_7PY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_6W5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f NTC_0002_0037_A23NMNVLT4_1_counts.tsv
rm -f 1136_7LE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_35B-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_7CR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7ZP-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_3FE-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_8C5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7G1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_88T-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7E4-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7U9-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_1VP-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f NTC_0002_0034_A23NMNVLT4_1_counts.tsv
rm -f 1136_0QH-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_7AA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1029_FSS-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_7J8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_84Z-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_3I9-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_8EZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7UR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7WF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7BF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7RQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_8AY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_1VE-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f altera_v3_variable_regions.bed
rm -f 1136_6IX-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f .command.run
rm -f germline_cnv_input.csv
rm -f 1029_BNK6-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_1I8-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_2S9-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_3FA-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1029_BTXK-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f NA12878_c_0002_gDNA_0007_A23NMNVLT4_1_counts.tsv
rm -f 1136_0L8-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_7F9-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f altera_v3_panel.bed
rm -f 1136_2PU-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_6K1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7ES-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f .command.sh
rm -f 1136_7NC-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_2F2-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_6L3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f NTC_0002_0033_A23NMNVLT4_1_counts.tsv
rm -f 1136_83H-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_6IK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_6O-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7FH-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_0KC-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f NTC_0002_0038_A23NMNVLT4_1_counts.tsv
rm -f NA12878_c_0002_gDNA_0005_A23NMNVLT4_1_counts.tsv
rm -f 1136_2RO-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_7QF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_3JH-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_6IQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_2E7-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_03T-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_6NU-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_7L7-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1136_6NA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f 1029_PAP-N1-BDNA-1_B237YJMLT3_1_counts.tsv
rm -f 1136_6JT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv
rm -f NA12878_c_0002_gDNA_0008_A23NMNVLT4_1_counts.tsv
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/f3e35de10d07e4df0a65c2c71147ed/1029_XI2-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1029_XI2-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/920a02c86bdadfed973a5f7dfec83c/1136_7WX-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7WX-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/b4bdf5010ee1f9d0e2b73c36d51a31/1136_7LD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7LD-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/eb01d24a30e7fa4ff3bbc986810182/1136_2QY-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_2QY-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/4fa43fafdd48686dc5b2d90b95c34e/1029_YCN-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1029_YCN-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/ea025eddca4fa3f008421ae12765bf/1136_883-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_883-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/287a75816c0bbfc849549bb73c1b26/1136_7MF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7MF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/544252250fecea4130201f9eedf4bf/1136_80B-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_80B-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/a68f88380f3148272b48e06e7acd6d/NA12878_c_0002_gDNA_0006_A23NMNVLT4_1_counts.tsv NA12878_c_0002_gDNA_0006_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/f37db98028de035d1437cfe35ac93f/1136_7PY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7PY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/898a0910cfddfd5db82e1573e2e2ab/1136_6W5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6W5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/b47450db8b0966e9a3bb7bbe82edec/NTC_0002_0037_A23NMNVLT4_1_counts.tsv NTC_0002_0037_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/3f3d3413dda5c26f2a6cdc7064f340/1136_7LE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7LE-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/111368568de080f570216e1d18210b/1136_35B-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_35B-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/2e33f38717195d62f08f84a66a9fbc/1136_7CR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7CR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/167d04c2d147c02afbbc8c2ba40a9d/1136_7ZP-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7ZP-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/d6219363e29fb32d0a45ed6465398c/1136_3FE-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_3FE-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/3307c84c8ac47d3d92fd93f6725f7e/1136_8C5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_8C5-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/fff33234babf9f241d01b1ac1df006/1136_7G1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7G1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/90f7347d18d4885b08b45317e4dec8/1136_88T-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_88T-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/6642d9a5789e3a575ef95e0960dc3b/1136_7E4-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7E4-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/59e96f0b0a7b17d0e54b8ee6b84755/1136_7U9-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7U9-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/187e1a520040a0bb8b5f3c4ba3064f/1136_1VP-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_1VP-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/ff7a1c43d90dcf41d808386daa09ef/NTC_0002_0034_A23NMNVLT4_1_counts.tsv NTC_0002_0034_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/1279f00ee47fb528d2cb3ccc37416a/1136_0QH-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_0QH-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/a68e539afe41148984c421ea059c8e/1136_7AA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7AA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/088b30c06e0b718845dd867cc0a1fb/1029_FSS-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1029_FSS-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/0bc66ca7facc69c1da65ed675ec28e/1136_7J8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7J8-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/b854919cc0db73541bc9130c275bb3/1136_84Z-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_84Z-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/afc0a27cfa337ee5a3952e8aa49457/1136_3I9-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_3I9-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/744388ab4a7fce9ad3b10bd198e7c7/1136_8EZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_8EZ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/5481821c54080995335cb8ee8d21fe/1136_7UR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7UR-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/139439c8d5aa14d3da5236cebeec53/1136_7WF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7WF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/39c2f60e9b7c426737f37da0b32723/1136_7BF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7BF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/851569f955b71704e30d17975e8aad/1136_7RQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7RQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/f2f01b8a458ea3d600ee921396466c/1136_8AY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_8AY-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/b13cd5f413e1c2786f866fd6738875/1136_1VE-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_1VE-N1-BDNA-1_B237YJMLT3_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/06/dca2cd9f0e393ab9e37d571ec1fc14/1136_6IX-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6IX-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/e8/94cbf090e73aa9da76416b97dccd91/germline_cnv_input.csv germline_cnv_input.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/17698a72c24fa02b4ae526fe38f883/1029_BNK6-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1029_BNK6-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/0c929815a2ae3b8e6fcc8820d28084/1136_1I8-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_1I8-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/fa318b3a87a5a0f9be219d9c1ad438/1136_2S9-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_2S9-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/3e08f4575fb39529c7f30aeb018236/1136_3FA-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_3FA-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/650455a684e930edb7796200e229ce/1029_BTXK-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1029_BTXK-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/125fec521853dd986ede32995601f9/NA12878_c_0002_gDNA_0007_A23NMNVLT4_1_counts.tsv NA12878_c_0002_gDNA_0007_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/703b1dc922066deaf79a28ee0be0ac/1136_0L8-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_0L8-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/b342e86b6772c7129de8e1959e3b8d/1136_7F9-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7F9-N1-BDNA-1_A23NMNVLT4_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/b1/2641cc73fbd7637b9c936ba0726b66/1136_2PU-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_2PU-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c40f57bfc0baad5d5185b5d40b6222/1136_6K1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6K1-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/ece27ea8109432d2943374a3de9d7a/1136_7ES-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7ES-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/a722374ce6c570acf5da9d5a36a123/1136_7NC-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7NC-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/f4755b8ae3afc922e055091715e291/1136_2F2-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_2F2-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/d668f683631fc330f27c63aafbd7c8/1136_6L3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6L3-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/966bcb0954881262fdb697a2d448a0/NTC_0002_0033_A23NMNVLT4_1_counts.tsv NTC_0002_0033_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/2056e2cf190ce1e37eeb93eb744d94/1136_83H-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_83H-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/e0e0ffe81969d53ed29bef7cacf257/1136_6IK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6IK-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/a0d90a166e8765472585a2af574822/1136_6O-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6O-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/9eb222f8df202fbb80158a8e6f528a/1136_7FH-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7FH-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/5e45f961a53c58ebd291ad4cc06252/1136_0KC-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_0KC-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/60c51376c6c4e9b48fb276c3c4467c/NTC_0002_0038_A23NMNVLT4_1_counts.tsv NTC_0002_0038_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/e018c7389d85cbcd7b1dc70c483a32/NA12878_c_0002_gDNA_0005_A23NMNVLT4_1_counts.tsv NA12878_c_0002_gDNA_0005_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/7a91a0d1a4597d57029f05bebc9492/1136_2RO-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_2RO-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/3307abda05869b7c2801fcfc6713f3/1136_7QF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7QF-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/9a223b53e26fa41a7352fdfdc2c6f9/1136_3JH-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_3JH-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/099338c4549038f2b14ef6aefe2148/1136_6IQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6IQ-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/beb9e0252cb03520d4295edaf3d5c5/1136_2E7-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_2E7-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/09df05f26bafce354428b062674a4f/1136_03T-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1136_03T-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/de7d173b8a072fee4315bc5962db44/1136_6NU-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6NU-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/efc0cb013b96219b4c01d3c373c564/1136_7L7-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_7L7-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/c5efeacf21dc5fd38ac302d7626a70/1136_6NA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6NA-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/8c3348e10be94666493728dd7913bb/1029_PAP-N1-BDNA-1_B237YJMLT3_1_counts.tsv 1029_PAP-N1-BDNA-1_B237YJMLT3_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/a09b2209e67797523784df94c45779/1136_6JT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv 1136_6JT-N1-BDNA-1_A23NMNVLT4_1_counts.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/51c6960b271dc29be852f70eb1f615/NA12878_c_0002_gDNA_0008_A23NMNVLT4_1_counts.tsv NA12878_c_0002_gDNA_0008_A23NMNVLT4_1_counts.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (77 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d counts_1.parquet sample_metrics_1.parquet ploidy_1.parquet B23H3Y2LT3_1__sex_calls.parquet B23H3Y2LT3_1__sex_calls.png" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/5fb84b9b25028695977080974e1a0c || 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/3b/5fb84b9b25028695977080974e1a0c/.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