#!/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/de/3eee02e445acf44a2e6aa2ce660996/.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/9d/c2895d10e99f094559795aafb52483/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 109/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/f1281541380f93d31bc06f3eedcd76/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 42/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/20df85f883124e702f6cf0e7e53195/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 34/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/576aaefbf94dfe012ddda2ec4e3eee/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 116/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/9c383469e319ff63f6a4c0b663ddea/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 7/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/e8203161f82fe8e681246e62d92ee7/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 121/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/fd2513e4a5e54d6801f2f503df36cb/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 60/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/c3352af9b1b137d8a5a3ba257d441f/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 171/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/3440cb1a5aca5631126b1719105e0a/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 187/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/2324d1619076126c32aabd478fb942/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 28/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/ac2bb025fb3b6d45d2d7c828f4c44d/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 127/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/f6d682c57d3f815f36283a11095997/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 173/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/a36c73e14c15b45ff09521be45f328/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 170/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/9f28e8d61b4564bb898b9067dcff4d/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 161/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/30cbf08ea79537bc411a10391f743c/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 26/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/46a0065d894f260add5cfd3e4fc8ac/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 159/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/dd7ba595e7ef24a58a2ed3720c35c8/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 27/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/6657bdab9cf2a1a3efaa054f9d62d3/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 41/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/85351d928324db8c2c2257c4292dec/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 129/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/484af7010a9361a43ab074ddc00522/1136_5BE-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv 195/1136_5BE-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/46361ce1748d1df4f73a1f2beb65ca/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 93/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/df49951d18148d55ae11159cc8d8ec/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 76/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/6dbd86c291d582c7e799e76fc40aad/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 12/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/54d1a5e24cb5da6a2aabbb2a3239d3/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 144/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/21f11d1e08c973fb5157bfca4793c6/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 86/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/21122e938141ecc4bde73acd0f88d0/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 108/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/263d831b6ff1ebbb468144cb02c138/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 49/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/70fd0b71eda8c56e118d4e248878fb/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 148/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/c1975284028f68652593e309945e9f/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 8/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/9ba7f927ceea54663164d7290af960/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 62/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/f7ef3ede5547b4b1466a0246ac15bd/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 51/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/4143a7833993e1cf0b9506b787185a/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 70/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/124274cbceea4e83c8cbe45ad2d365/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 155/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/3ca6dcaf75c50cc22714a550575322/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconfliction_audit.tsv 198/NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/7aaac299e2417ec7ca415e06e5b061/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 58/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/4704df26bf9c204addd546535b9e0a/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 140/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/b6e4705d384db0af107094b3aedb20/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 83/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/985901261dfbd04e0a92496b131e98/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 138/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/6d375a738a7204d6c26757ab7081c7/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 189/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/f4f24bea237ed134ed2515512885be/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 54/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/a0f68fe143215f5cfe56a9ffa9dde1/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 128/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/c4559f7b98b84e0b0e829cd6826249/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 4/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/855df52c9e7d45b2cec09af0a83fd7/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 103/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/93865aa1a87a94ca1c6f6f9053e613/869_XA6-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv 192/869_XA6-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/81a9e802ddd8c3cdc6e82d1f589d34/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 40/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/79eef47544e00414dfb9b074444255/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 118/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0312b03ed3209d94baaffdedc4f3b6/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 13/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/ed62d3bab5bcf79d71511f71868720/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 61/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/955019a2bacbe9c9b6293764c5c01a/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 111/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/adff3578bef07d2d4fa4dd94aa08c7/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 39/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/7d1445582d399329af2a67ae75fe99/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 69/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/87894984356d6f016dff43712ac971/1136_7L-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv 190/1136_7L-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/37f2d45ab0295a7039f42cdacba7e5/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 97/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/18a276f7734cb10cbd927eef2a5a28/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 114/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/d48bf3e1c8091872f9b5229f304ea1/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 179/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/699383cba0012e30902351e80af70d/ngscheckmate_all.txt 45/ngscheckmate_all.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/40debe84f90733b0aca7b0bc803f00/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 71/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/cf17a8b02040a0cf264c195b67e5c3/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 131/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/f179e2b462a690260dd0171b3bf276/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 101/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/c0ffd56e17081c98384b8740e7f6c8/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 123/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/4f46440aef2465345505316d76a787/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 168/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/9243c1a37e38903bd2b01a1f9a9b8b/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 38/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/04eb5091662624a0627a87de6e3a95/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 120/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/c71edef76261e0ed251cbc386375ab/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 14/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/d4fa5d113a359610df683cea175f75/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 25/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/4b85288240a0fc1f68372dcc031ff2/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 55/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/adfa3248f7e4ebcd54671c2a3fb5a2/1136_7OO-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv 197/1136_7OO-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/f21d1fc75cc3f057e4a7e7ed04c398/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 30/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/7427a7f5f32aa2333bacabb5c7112e/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 52/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/a0d5d62c1464ed0c68b09ae0fed0fc/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 90/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/19df49425375e2436c381550dfaa89/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 188/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/bf81baeaa5685b00805ebaf8cc696b/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 74/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/e682c532a263ca01f62d55031da637/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 112/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/280aeb48d1fb1668c2e0aa84f07463/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 48/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/528061ddfb7df1597b85732603f0b4/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 89/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c00a302f2b7fb7e4298f76f3e003b5/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 5/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/8a1f82b571f0afe635b8a7c5de40cb/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 15/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/724604cbc6e7eb97ddbd0f4c794559/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 56/1136_7L-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/3eee02e445acf44a2e6aa2ce660996/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/149b995e73a928cd24fbe5f369bb93/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 150/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/40bcb6331bda4db5567d347433db74/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 166/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/7926fb143d5cf2975e7fc82fab8ab8/869_HUS-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv 193/869_HUS-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/74779e35e9f859a3542525f74c09cc/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 104/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/0994dd6fe717aa2394ce274cc95339/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 146/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/87f5f18cce090067392898b7447e47/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 88/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/2b9466a2ac84451d0560866a46351f/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 65/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/38d390db30e2ee4520ca23cb04b0b7/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 154/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ed5bd9e6afd8038dd6fd9a192ff7ae/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 29/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/6e619ae21f879867e1574eeb817c8d/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_snvs.bcftools_stats.txt 177/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_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/75/e16d849f2999ce10009b6b22158152/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 75/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/f0644e0f42ed8781ab783271156931/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 153/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/91372defd28b70d3e1c8c9c714042e/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 169/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/56585caf0b9debb217ee31422899d7/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.strelka.somatic_indels.bcftools_stats.txt 176/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_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/bf/ed91fc9e0a6805624c565ddaaebf47/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 85/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f0616a2e231bd07c8df3b270cc9f2b/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 94/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/c47eabef3cafaf5b010c6b8cbedc4c/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 141/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/6f87e5088282629005402e9a4b755a/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 160/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/6fcca5585d027345e2e607b5863142/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 147/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/16b8dec24f4fcebbd1c2441cc55d0a/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 119/869_XTN-T1-TDNA-1_A23WGJTLT4_5_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/b9d9dc5902485a7a87ccfb92ae02cf/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 174/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/f5f04b01f546593fb0fc79d564520f/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 9/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/a5a0295d12362a92b0ab7ed33cb2cb/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 32/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/d76c50ea3084a74a01da9fb7b26ffb/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 16/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/b908677a54ce232261d1de2b344673/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 184/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/ce710c71febeb8ef6bba27308da28a/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 130/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/7e5f9c5950c6d13286d6ed4b45b8ba/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 82/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/ee6b422429ab59e4c48038ac9dee31/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 91/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/3d4fe2085a768768776e5b92b1c597/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 180/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/2e4e7219ef719c4fea5e09e9f05a51/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 164/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/30337ebef6ab1f299cfb8d983a50c7/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 17/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/a087425df14f8754109f1146dc92ec/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 99/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/369720d38ad9496a27bf2d0d6eccfa/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 133/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/3f5df81df7d024c60eb6c161d31211/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 163/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/ea5824adc0b6c0ccce94f85378bc68/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 182/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/0912b16295f85629021e3417f33d2d/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 162/869_XA6-N1-BDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/adbbc31b9e71ffafee14c4d83668cd/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 126/1136_5BE-T1-TDNA-1_A23WGJTLT4_5_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/50f57912d947d0e4d90bc61ba90f88/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 80/869_XTN-T1-TDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/7a65ba11882d2f9dc850dce83bfa15/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 107/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/00597112a24a4622a081420764d7a4/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 43/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/c7467d9789cc396827a776ea3d388d/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 135/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/80e349bae3fc0273f39f74a202a6e0/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 149/1136_7OO-T1-TDNA-1_A23WGJTLT4_4_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/1fe9c7cdf2b62777316d74e13ec13b/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 50/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/787d7226ea77940644f468e965b8de/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 181/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/0110748f733ec0bec5f059ab734085/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 100/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/c7ef10b5c628dc56355697a33640ce/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 134/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/7d51cdfa12d6b0e4d7c629d4c781dd/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 124/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/19c85940338f4e4718a737fe944100/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 175/869_VZQ-T1-TDNA-1_A23WGJTLT4_5_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/c325f5391afe919604b410cbea8e67/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 10/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/c497006298c1ad9357402c229c3020/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 79/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/010f74744895eb4b9b4289a38bf27d/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 96/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/a3e16ea271d51f3b5d0a60b96f979b/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 178/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/dc37bf14df80acf6dec038c5883726/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 102/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/15f1703b78e691c0494a971ea9fd5d/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 151/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/42e87701f264103fbf52e1c7425d2b/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 35/1136_5BE-T1-TDNA-1_A23WGJTLT4_4_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/3eee02e445acf44a2e6aa2ce660996/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/5cf1f64b9244c71804f95b54d18628/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 115/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/ddb8c308ebd0a356cd715ad08ffa58/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 1/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/6cedb1a39fb3a2d037bd719e718623/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 33/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/0523efab254adf8d534fdde6ec5620/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 81/869_VZQ-T1-TDNA-1_A23WGJTLT4_2_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/0b7e9e6f7754a5bf2b7871f2a69a18/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 156/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/7be203fc9e248eb656dbbbaaf1bbab/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 110/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/7b2bbccb9401232a70d03f7244db25/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 167/1136_814-T1-TDNA-1_A23WGJTLT4_5_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/5b41982ba82eb770d2534d85be8418/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 186/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/a09ca8b8de859e759656ac4918c698/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 23/1136_7OO-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/e29248727d2681547d85be9f0922f1/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 78/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/11bfd400fb7739f0e40c50af483f67/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 117/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/d8b1d737a74b112618b878a635c017/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 95/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/d55f8bf69a9489dbf0f61c1531bed4/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 139/869_VZQ-T1-TDNA-1_A23WGJTLT4_3_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/11a89d31607a494230db2f1aca0074/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 125/1136_5BE-T1-TDNA-1_A23WGJTLT4_3_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/a8a5dd82676c4065a5eb67d501b05f/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 63/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/53cca2e10951523f95ef5c42f49951/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 152/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/0817014ccfca9f532c42e52299b1c2/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 87/869_VZQ-T1-TDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/90fb4b9318416a1f5c8eaca93168e1/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 20/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/a30254dff7874ab9cd3c679b065421/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 22/1136_7OO-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/ae9e00522a24e0ef68cbbeaa6c6a97/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 31/1136_814-T1-TDNA-1_A23WGJTLT4_3_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4ebc5b5236ac32c566b6d51e2901c7/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 6/1136_814-T1-TDNA-1_A23WGJTLT4_2_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/098f8a5f13457f9b03ac8bc67c6410/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 67/1136_5BE-T1-TDNA-1_A23WGJTLT4_2_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/d5a6970715a84ba49b586021446b55/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 145/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/9204b8fb3625a8a38d87aac524526b/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 106/869_VZQ-N1-BDNA-1_A23WGJTLT4_1_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/1d17e6add7cafa629d5fc6b0ac1cb6/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv 191/869_VZQ-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/ebe11114110829b11e272cf0ac5ce0/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 136/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/52d1da0e182a65de51c1d4ffb13ed2/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 142/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/97dce89ab5d2049854442f5d2f6093/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 59/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/1c0eef70b487be846640f3e90706d0/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 72/869_XTN-T1-TDNA-1_A23WGJTLT4_3_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/5a981eed9b28b65f401bfdc2996f3a/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 92/869_HUS-T1-TDNA-1_A23WGJTLT4_4_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/95a36d97e50147ab8215a6c62428bb/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 165/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/224e1757f6c485a50ef5d063edc588/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.conpair.contamination.txt 132/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_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/77/7f400a84f8d68a89ef5d1b32763d4d/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 19/1136_7OO-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/1401f2e17a29ba6b40987b1c662cf1/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 68/869_HUS-T1-TDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/151b79a9a9f9f84ffc7f2dedbd0c42/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 47/869_VZQ-T1-TDNA-1_A23WGJTLT4_4_vs_869_VZQ-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/55657a3917ba78be7d7f750852675e/1136_814-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv 194/1136_814-N1-BDNA-1_A237CFYLT3_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/bbfe2eb4f74bbb75868a753ac8a50c/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 105/1136_7L-T1-TDNA-1_A23WGJTLT4_5_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/15ccb23435a2fea1ed2e6b99aac974/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 24/1136_7L-T1-TDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/20a46f54bc74dfc63dcce7491fb069/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv 172/1136_814-T1-TDNA-1_A23WGJTLT4_4_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/e6251ec8ec9926cff3167a3724b9d6/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 122/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/80758a0bf78e63f936a93a4f9eb49a/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 53/1136_814-T1-TDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/23e4354ca339feec75bbcabe565c2c/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt 158/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/50e7cda6ebffa7a97ad3d9a3ce72a5/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 2/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/9d68c2a75b3b5f24f57ec40f2434c1/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 77/869_XTN-T1-TDNA-1_A23WGJTLT4_4_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/0c404e9db7358ee9c45f21228fd1e0/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 84/869_XA6-T1-TDNA-1_A23WGJTLT4_4_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/ae32cff149d2cbd49b30d8a28e8aeb/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 73/869_XTN-T1-TDNA-1_A23WGJTLT4_2_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/12c8f4b7cacc56770d2a038ea2fa7e/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 11/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/0bb1ab1f9f85ff2b0800b15f82ec31/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 183/FFPE_HD789_01_p2_gDNA_03_A23WGJTLT4_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/86/4203a0aa6faf6916fcd77ce227a351/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 37/1136_7L-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/a53cb672aba1ea95a30b856c0ebe57/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 3/1136_7L-T1-TDNA-1_A23WGJTLT4_2_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/92e97e1c849cf59774606bfb9932e9/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv 66/869_XA6-T1-TDNA-1_A23WGJTLT4_3_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq.filtered_snpEff.ann.tmb.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/d758c32fa67f3dfcd29855859adfcf/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 185/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/6d4853279abed4a97b27e28720395c/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 36/869_HUS-N1-BDNA-1_A23WGJTLT4_1_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/5dccd0b6907d76c844f9247fe01412/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 157/869_HUS-T1-TDNA-1_A23WGJTLT4_3_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/995a3af33124484a34d5074955e06a/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 18/1136_5BE-T1-TDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/8d50fd9cc8c5a853ee452f5c2859f4/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 113/1136_7OO-T1-TDNA-1_A23WGJTLT4_3_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/39d22ad093024bd3ca012aeefaa8eb/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 57/869_HUS-T1-TDNA-1_A23WGJTLT4_2_vs_869_HUS-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/16824d8c4105426617c7b406f2ec7e/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 64/1136_7L-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7L-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/e7f491e8bbf6d2bd0782265c3b8d92/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt 143/1136_814-N1-BDNA-1_A23WGJTLT4_1_vs_1136_814-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/2d75ec4bc0efd5bbf8f4adda021e34/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 46/869_XTN-N1-BDNA-1_A23WGJTLT4_1_vs_869_XTN-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/f9764d26790b74b9d689f14dd9742a/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt 98/869_XA6-T1-TDNA-1_A23WGJTLT4_2_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/908e1f7ddea1106bbec4153e6042ca/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt 137/1136_7OO-N1-BDNA-1_A23WGJTLT4_1_vs_1136_7OO-N1-BDNA-1_A237CFYLT3_1.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/aacfc9a3c9adcf169e77fca469a367/869_XTN-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv 196/869_XTN-N1-BDNA-1_A23FG3YLT4_1.deconfliction_audit.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/e92d7275b2a6a33abcff5eab624202/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt 44/1136_5BE-N1-BDNA-1_A23WGJTLT4_1_vs_1136_5BE-N1-BDNA-1_A237CFYLT3_1.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/1db5557025a13ff05c761f5fa64c35/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt 21/869_XA6-T1-TDNA-1_A23WGJTLT4_1_vs_869_XA6-N1-BDNA-1_A23FG3YLT4_1.conpair.contamination.txt")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (200 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/de/3eee02e445acf44a2e6aa2ce660996")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/3eee02e445acf44a2e6aa2ce660996 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/3eee02e445acf44a2e6aa2ce660996 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/3eee02e445acf44a2e6aa2ce660996 || 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/de/3eee02e445acf44a2e6aa2ce660996/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/4c/bf7b87e705678986c766bbb91a7e68/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