#!/bin/bash
### ---
### name: 'NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation)'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/multiqc:1.25.1--pyhdfd78af_0'
### outputs:
### - 'variant_qc.json'
### - 'versions.yml'
### ...
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/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d/.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/4e/b748ff8024669e1cee8f076e272bdd/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 22/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/5d5a7872d09553abce1d92fd9e0c32/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 163/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/7fbbd8bf255c488f8b68f166c09b59/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 17/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/7c38bc161d943b679c04cd1db70bf1/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 50/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/d9fdcb4e0904bd8197eb45171fdb16/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 156/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/fcc39180855c704fdceee12f337407/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 140/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/8a63052348dff58f7567dea82039d5/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 87/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/472ca0aced417bf6388dd1ffaccc02/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 6/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/fc13db1e77679d78a5380067113422/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 49/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/5de89e745fcc7340d62e9fc7764718/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 67/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/c943fadf6c27f5a7e54e824735f1f0/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 116/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/36fb36abe6c9dc0feb1a558c26df64/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 99/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/96885a2e586bf1662c6d7089cc33ee/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 103/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/f049ca0c96d739a44a4a718976e6b4/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 120/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/30ba9b1f030781deeb6b5426496d99/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 16/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/367e229735a7660ab0aa807af4adf8/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 96/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/887fbb366b41e52a03849536453af5/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 102/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/efe2cb68cd5c13d2852f4726b053fa/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 143/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/5946e21f62982ad19cd08df3bd9847/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 55/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/709e6cccf0aaa47adecdd025600f17/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 78/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0e65f4d7090c88145adea1b9bfaba7/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 169/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/6c7907db404388a11d17ec0910dcf3/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 114/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/5f2e3847408cc652dd0aceee0552ab/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 159/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/bb34ddaa6d67d65f6a2373db083bf7/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 132/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/361ba5752e37b3fd829349f3d69800/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 167/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/559964c2c6d0c94720632ff8262efc/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 92/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/166483064572a7641da01b224d5aec/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 131/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/62913fd195750e332847590f2aa8e7/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 176/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/9314d0eb70da7fb6e9b907a88da198/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 66/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/473e9ef32e670d12d8b54030852894/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 74/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/28ecba9957b61549679f8aabae595a/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 51/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/cac7a322ff30704576c5fb22596577/ngscheckmate_all.txt 56/ngscheckmate_all.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/c2477e62a4ac9b915d675fb1665a37/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 98/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/8f982f75696418c206545618f3daaa/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 105/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/3e4741b9a849ffd7996a78e7e6b96e/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 41/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/798ccba9b5c31cb0d11daeb149d9aa/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 166/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/af34358aca87472802f9025783a5d3/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 42/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/437cf10485a9a2960f6f6075be2419/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 141/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/4c4f7ecaf879480d53f9c2ac1aeca5/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 188/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/a68f30551e3f6859b0e53ec0bb732e/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 147/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/bcb6f27fb2db6bf73aefa146fd23e0/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 100/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/90a12d08a3abe84633c0c4fea93a34/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 81/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/03847fd79732b6fe44cb53753305bc/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 68/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/9f29f54d67eedc57bbdc1db1de6266/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 53/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/805043b5591a03b036bd1bf711ba29/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_indels.bcftools_stats.txt 189/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/7798575e8cffb3cca47a6215c3bf38/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 62/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/6d1ec5abdbd2e18f61a52c92732136/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 97/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/92f73b0dca793ed1026e55ea6e7e5a/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 127/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/03ac1785f44ece8973b18ae91c7c91/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 34/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_7_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/b29db23c3e5bebc5048a715d0afc75/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 122/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/7d2fefbad3fdadc1da3fb4f5e6b429/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 10/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/6ae4753083776200d874cb04f72628/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 86/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/e5326b91f492c30b86391e2dcaa96b/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 162/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/599964520ad27368ed71142d2b78b3/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 14/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/2c159f1c38bfdf15a05f6281ebea47/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 38/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/e4969163e3b7b4901a22d4c5e0b3aa/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 11/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/070f62637df38715aaa193d9818ab1/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 20/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/efd8aa7f849c75cff1382f73dccd6e/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 69/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/06079f1175ba63c14b301feaab1f77/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 170/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/8950ca359fbf3a40038cf586998320/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 52/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/312f9676974294d8af0de0fd780fa3/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 80/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/d33c10318e06421008bd3371a21932/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 107/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/a1e635f4f387f617fbaa46f99563f7/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 45/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/5171af3983035aead1d316f1875480/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 23/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/7555167ebfd584988bc1a5d5555e35/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 184/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/fef0c7560eedcf2a590e9de091a4e2/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 180/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/1a448d801e403f5b5324ea6b871a97/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 190/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/de02e0a6ae288cbacc3a292c2afe2a/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 29/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/a329882c94f1ece980ff8214e3bdd4/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 134/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/fc1c49a23e52db8a0d293c2465834a/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 25/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/29e9f64457aa05f56d0671d6c725e7/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 152/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/15d4ca89979e55fac5b65ca856fe16/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 128/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/59facd644b2d4414441bdb986e33e6/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 37/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/f176636b306069997338513ef4f2bd/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 32/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/300acbb94eb5d3eeaee2871196f632/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 15/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/a30c404cf6f790a4b52cda6c52118d/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 65/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/a962660e13b783ec238a726c817981/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 145/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/a79093ac766f2d199d139379663f5e/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 173/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/57d6b446b7e6dc410fa3837256cfe1/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.deconfliction_audit.tsv 195/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/0d39cb5b9bbf1e3c9b7e47f2973320/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 149/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/e4ace25ce0a6c109654dc40eea9dc3/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 88/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/670d2b1f019c869c96bd4b96bb7806/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 108/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/bf0831ecc4e40405ed8fc6ca17f893/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 157/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/9041823a7a6bb1768f613f03a9575f/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 93/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/06c0046f183fff1c2d51f979965f35/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 76/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/9d921930c245c3094edd3b32dece0c/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 2/1136_5WB-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/907aff94fd472dd61f6995bad6a2cc/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 59/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/fb3f982d72ff35e556ae7cb2f6dcf5/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 43/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/045da5258b1ef209f7496b522910f3/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 31/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/fc33723f29b1bdd55e19cd65c70bd1/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 12/1136_6I8-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/1290642f51c9ffd69c527ff3abfba4/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.deconfliction_audit.tsv 194/1136_5WB-N1-BDNA-1_B23KFG5LT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/2022e987059efc0c05aeda3b2d646c/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 123/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/838b5bae5c0737918fdeaea1d5dad7/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 168/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/4b985b195ef45b9ed9e9c4800aefbb/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 33/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_4_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/ca5647cc21b0824e5ff7412931aebf/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 64/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/e8ee9a5dc9a08826875eab5faebb4e/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.conpair.contamination.txt 89/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/7aa0bbd83cb24c86b0d6571e2e68ce/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 133/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/897e10e142e6c7a4ba0b192641b233/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 9/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/25ff4af43535f60ba2390bc551dff9/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 26/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/939000185ad1b2d041a58c5d28d63c/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 28/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/4bb91f9ddea704c15079df90c0fbd0/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 135/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/e18ac7c2dd63ef09a89e40e8a68ab4/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 150/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/6ad67f844260d7278356739adea3d5/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 153/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/a1a89768cf7d0ab16b8f018ed7e682/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 73/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/a20312cb8e31d6f9d5dfff06407c9e/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 101/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/69f43eb9681c2f88dec1840bf79df8/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 21/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/c6c8be98793bb0eccc94d8ea2a4591/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 57/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/1a8477921dc1fa9342d13227df3ebc/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 4/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/85da6686e5d544865196998858f225/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 70/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/1e32795b6c4a0ef3a9365b7529d04d/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 54/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/f4e8a96778806acc0ed3c30961a35b/1136_6I8-N1-BDNA-1_B23MHTGLT4_1.deconfliction_audit.tsv 193/1136_6I8-N1-BDNA-1_B23MHTGLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/750800a448acc6399ed83cead65ab6/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 111/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/7f91ea25c1cfeadf2d588fe1694330/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 121/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/e4573bfd8881c62e403c4bf4f56465/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 179/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/c33608030bf1448d2ad4d483b0f83c/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 151/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/e04aab21d791739cf92266156a0409/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 46/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/7b3462b3d1e3aa33d8c3da22e2231c/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 19/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/7be9b07220d834d92c785243f17ff2/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 95/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/a4940109781fa6518991a93797bd5a/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 186/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/3770e4a5998361e6e47fb923c35327/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 40/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/9e4679093b8c2a58cdc4c1b14e03fe/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 58/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/85a2392bec7e8cad446274282f2ecf/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 137/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/1c7fd1574fdc1f4a3e1811d3a06861/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 77/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/c6f796b7e94e743754a4811cf9c4f0/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 130/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/20c22423899ecafd5a95213ff108fe/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 7/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/c95d6a87d7a8c1e415c60e232aa321/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 172/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/5e283b94956c302acd6f8b0290d103/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 142/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/20d07484ef1496d39e55bb17648304/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 160/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/bf0b5577467d362dfecbb17fff2661/1136_85O-N1-BDNA-1_B23KGCJLT4_1.deconfliction_audit.tsv 192/1136_85O-N1-BDNA-1_B23KGCJLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/d9dbeee7f1d5f375de7a8815a57337/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 90/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/3ac49edc69f71be45379fb3960a959/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 118/1136_5WB-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/74ddf03dc9aa5c2285ecd928de4b9f/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 161/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/be03ebeb8007f1d3c3fdf6508522b7/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 115/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/939d65819db061aacb013a1166cf41/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 181/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/f0f84472cdfc75783dc1d72ffc7058/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 183/1136_85O-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/f3f534942df429cd0b68e050690944/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 18/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/be8303b37202faf2bef54ff5d6e62d/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 110/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/5d5427d933d00fb85f15246a7b029b/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 13/1136_85O-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/6e240fc3feba0b97e57adc5c912de5/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 125/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/c5c71e3977adbc80fcaea2b5836b1a/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 60/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/05955be323ec0e3daacef040b4d726/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 113/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/309291a4818706517812da88f39d4d/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 165/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/95f471e58285e72554769d171bc2d8/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconfliction_audit.tsv 196/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/777f91f006e84ae8df16fee3190138/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 106/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/d0a6a1bd7f01bf5790a5c65b6f23d9/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv 174/1136_5WB-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/e9660ffff38c624b12320ffb9c0411/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 171/1136_85O-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/804824362be09d9b4948b6abd6c873/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 154/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/18a080f654d923dcbc7a7ddf8b5612/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 24/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/11ef4c6a7a88a35e4d07caa386b1a8/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 175/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/2687705f020aef1786824051624ee1/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 85/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/885b7f1528db09ab0fc37681a3dea5/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 48/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/6f79e6f0f17efbb5c97d92f34c6947/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 146/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/1e284c8a7cc87a684a1c6edf1646be/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 187/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/14432f96ad22ee5ccb3d6cf68dda59/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 178/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/014a690665b511c0acf8abd6dfeec7/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 61/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_1_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/ddfe9b423cfc1e23bacce6c969a710/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 109/1136_85O-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/6afba36595daa5839069354787f9be/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 8/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_9_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ff56879eb093f2c2339868a7461242/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 139/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/cbbe2b1378efdcb381fa1be34e8e73/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 36/1136_5WB-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/4087ae9c8e61493c86adda973d29f3/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 124/1136_5WB-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/bb5da75e345d18d0d7ea2be29fa22e/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 91/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/ff676a28f1bef2c3f5dfbf13624226/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 79/1136_85O-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/6fbf5fb1fe9e500711e8eaad034705/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 126/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_5_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/15bd2d6a05ba2f5bdc4348ecdc8f2b/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 94/1136_6I8-T1-TDNA-1_A23WJ5GLT4_7_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/fcab3229bd9e5a7cf2f3f55280f249/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 185/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_8_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/b505622879798044c03a05981cce4d/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 164/1136_6I8-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/3c2f0688607ced194fc804b5138cfa/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 117/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/76a4af9a09131f4a51a1fc5e4651a1/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt 138/1136_6I8-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/fb2a834b7847a7b690d808e64c8f3d/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 84/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/4692468a3609764d19dffb55d4ccaf/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 158/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/122037782ac2010188d1d2c2026b95/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 129/1136_6I8-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/bfe4f07b42efbc019df9f02d4d3e24/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 63/1136_6I8-T1-TDNA-1_A23WJ5GLT4_9_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/43231e42577228276516252484542a/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 119/1136_85O-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/348d26b5046cae11e581475e3f6d5b/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 39/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_1_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/d5ecd2ae865ecf55a6b60adfd6eff5/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 155/1136_85O-T1-TDNA-1_A23WJ5GLT4_5_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/3a78f916f4c8b826dba99a0f210bf4/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt 72/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/e8d096b741d393ba69cad278755623/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 112/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_10_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/270101272615ed5c243829a3728fb8/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 148/1136_6I8-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/50475cba533a0a50f9ef3727d7b464/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 5/1136_6I8-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/c574c980553715e3c2353010f493ef/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 30/1136_5WB-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/7a25f3e3e44264a0ae41e0db34476a/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 47/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/b72c34f86cbbc52945c91c3897289c/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 75/1136_85O-T1-TDNA-1_A23WJ5GLT4_3_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/94b6326b99cdc9b0caf0b5302c06d5/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 35/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_3_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/6e837c004df2654c9cde927e041df7/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 191/FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/48a335fda3d0ee6d6e96a164b3cd6e/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt 27/1136_6I8-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/34ba78f8a1e47e793e5c2a5ce42a60/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 44/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/d532f5dcd8f40db18d34bfbdebedde/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 71/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/741cd1d7bce2924c9d6bf835667544/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 136/1136_5WB-T1-TDNA-1_A23WJ5GLT4_4_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/ab2d7b720af22d06b9ffc086934f4c/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt 177/1136_5WB-T1-TDNA-1_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/ce7782e68921fc76d3775fdac91d25/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt 3/PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/05eb2f995f9608d713c1e3a7e444e1/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 104/1136_5WB-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/977338f300dd98bb4ac7c79b6a248a/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 182/1136_85O-T1-TDNA-1_A23WJ5GLT4_10_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/76ea81b6ea12b4364fd08afe489819/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 83/1029_BTOJ-T1-TDNA-1_A23WJ5GLT4_6_vs_1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/34d873cd0a7b359201160e98d8206f/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt 82/1136_6I8-T1-TDNA-1_A23WJ5GLT4_6_vs_1136_6I8-N1-BDNA-1_B23MHTGLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/7ef0b2a32f3b4cbd9257725ea48858/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt 1/1136_85O-T1-TDNA-1_A23WJ5GLT4_8_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/1e52a868a1a44b5dece29368897212/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt 144/1136_5WB-T1-TDNA-1_A23WJ5GLT4_1_vs_1136_5WB-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.bcftools_stats.txt")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (198 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d variant_qc.json versions.yml" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d || 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/4e/12aa3ccdb1139ce3e5ab7ef19f5c5d/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/82/99cabdeff5dc187da610e64505baa0/bin/*" $NXF_SCRATCH/nextflow-bin/
chmod +x $NXF_SCRATCH/nextflow-bin/* || true
export PATH=$NXF_SCRATCH/nextflow-bin:$PATH
export PYTHONNOUSERSITE="1"
export R_PROFILE_USER="/.Rprofile"
export R_ENVIRON_USER="/.Renviron"
export JULIA_DEPOT_PATH="/usr/local/share/julia"
[[ $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