#!/bin/bash
### ---
### name: 'NFCORE_SAREK:SAREK:MULTIQC'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/sarek/multiqc:1.33'
### outputs:
### - '*multiqc_report.html'
### - '*_data'
### - '*_plots'
### - '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/fe/eea7cffad6ad43857ee9a84a319300/.exitcode || true
set +u
rm -rf $NXF_SCRATCH || true
exit $exit_status
}
on_term() {
set +e
[[ "$pid" ]] && nxf_kill $pid
}
nxf_launch() {
/bin/bash -Ceuo pipefail .command.run nxf_trace
}
nxf_stage() {
true
# stage input files
downloads=(true)
rm -f 54/HCC1395_BL.TsTv.count
rm -f 4/Sig_18_Blood.stats
rm -f 10/Sig_18_Blood.mosdepth.global.dist.txt
rm -f 11/HCC1395_BL.mosdepth.region.dist.txt
rm -f 81/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.qual
rm -f 6/HCC1395_tumor.stats
rm -f 41/Sig_18_Blood.bcftools_stats.txt
rm -f 8/Sig_18_tissue.mosdepth.global.dist.txt
rm -f 65/Sig_18_Blood.FILTER.summary
rm -f 74/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.qual
rm -f 80/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.qual
rm -f 89/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html
rm -f 71/Sig_18_Blood.deconflicted_germline.FILTER.summary
rm -f 2/workflow_summary_mqc.yaml
rm -f 57/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.count
rm -f 76/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.qual
rm -f 34/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff.csv
rm -f 52/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.count
rm -f 73/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.qual
rm -f 5/HCC1395_BL.stats
rm -f 23/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html
rm -f 43/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.bcftools_stats.txt
rm -f 39/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.bcftools_stats.txt
rm -f 21/Sig_18_Blood_custom.ann_snpEff.csv
rm -f 85/variant_qc.json
rm -f 28/HCC1395_BL_custom.ann_snpEff_VEP.ann.summary.html
rm -f 58/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count
rm -f 9/Sig_18_Blood.mosdepth.region.dist.txt
rm -f 60/HCC1395_BL.deconflicted_germline.TsTv.count
rm -f 3/Sig_18_tissue.stats
rm -f 84/HCC1395_BL.deconflicted_germline.TsTv.qual
rm -f 25/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html
rm -f 40/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.bcftools_stats.txt
rm -f 90/HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html
rm -f 17/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff.csv
rm -f 53/Sig_18_Blood.TsTv.count
rm -f 79/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.qual
rm -f 47/Sig_18_Blood.deconflicted_germline.bcftools_stats.txt
rm -f 83/Sig_18_Blood.deconflicted_germline.TsTv.qual
rm -f 87/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff.csv
rm -f 68/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.FILTER.summary
rm -f 75/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.qual
rm -f 62/custom_Sig_18_tumor_normal.manta.somatic_sv.FILTER.summary
rm -f 18/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff.csv
rm -f 36/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html
rm -f 1/methods_description_mqc.yaml
rm -f .command.run
rm -f 16/Sig_18_tissue_vs_Sig_18_Blood.conpair.contamination.txt
rm -f 67/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.FILTER.summary
rm -f 26/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html
rm -f 70/custom_Sig_18_tumor_normal.strelka.somatic_snvs.FILTER.summary
rm -f 86/variant_qc.csv
rm -f 22/HCC1395_BL_custom.ann_snpEff.csv
rm -f 37/custom_Sig_18_tumor_normal.manta.somatic_sv.bcftools_stats.txt
rm -f 48/HCC1395_BL.deconflicted_germline.bcftools_stats.txt
rm -f 49/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.count
rm -f 82/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.qual
rm -f 7/Sig_18_tissue.mosdepth.region.dist.txt
rm -f 12/HCC1395_BL.mosdepth.global.dist.txt
rm -f 33/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv
rm -f 59/Sig_18_Blood.deconflicted_germline.TsTv.count
rm -f 38/custom_Sig_18_tumor_normal.manta.diploid_sv.bcftools_stats.txt
rm -f .command.sh
rm -f 35/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html
rm -f 50/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.count
rm -f 64/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.FILTER.summary
rm -f 42/HCC1395_BL.bcftools_stats.txt
rm -f 88/HCC1395_BL.deconflicted_germline_custom.ann_snpEff.csv
rm -f 69/custom_Sig_18_tumor_normal.strelka.somatic_indels.FILTER.summary
rm -f 19/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.csv
rm -f 55/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.count
rm -f 13/HCC1395_tumor.mosdepth.region.dist.txt
rm -f 29/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.csv
rm -f 45/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt
rm -f 14/HCC1395_tumor.mosdepth.global.dist.txt
rm -f 63/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.FILTER.summary
rm -f 31/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html
rm -f 61/custom_Sig_18_tumor_normal.manta.diploid_sv.FILTER.summary
rm -f 51/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.count
rm -f 27/Sig_18_Blood_custom.ann_snpEff_VEP.ann.summary.html
rm -f multiqc_config.yml
rm -f 20/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff.csv
rm -f 15/HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt
rm -f 72/HCC1395_BL.deconflicted_germline.FILTER.summary
rm -f 77/Sig_18_Blood.TsTv.qual
rm -f 91/nf_core_sarek_software_mqc_versions.yml
rm -f 46/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt
rm -f 56/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.count
rm -f 30/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv
rm -f 24/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html
rm -f 32/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html
rm -f 66/HCC1395_BL.FILTER.summary
rm -f 78/HCC1395_BL.TsTv.qual
rm -f 44/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/18e99a1be623ce1767644b9e7d4e23/HCC1395_BL.TsTv.count 54/HCC1395_BL.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/6561590a1a4ae0acc4b8fe120d0865/Sig_18_Blood.stats 4/Sig_18_Blood.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/ef556635cfabb55003e7e128d96e16/Sig_18_Blood.mosdepth.global.dist.txt 10/Sig_18_Blood.mosdepth.global.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/99a8f59a170719ce35ea54ce1122a2/HCC1395_BL.mosdepth.region.dist.txt 11/HCC1395_BL.mosdepth.region.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/4896a221e2ccbd7792862e636738b8/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.qual 81/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/a00104c435edb83aed2e224f8b539e/HCC1395_tumor.stats 6/HCC1395_tumor.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/790ee74c351b8ef50d0c8c1a3b4508/Sig_18_Blood.bcftools_stats.txt 41/Sig_18_Blood.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/dbfce516f006a5d9292f311a18f2ba/Sig_18_tissue.mosdepth.global.dist.txt 8/Sig_18_tissue.mosdepth.global.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/3c1ee2f78ad16e872d3984d2e2a8f5/Sig_18_Blood.FILTER.summary 65/Sig_18_Blood.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/4da6c58d2d665d38eed0aee0af4bfc/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.qual 74/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/089071bea702f69476de73d2da1299/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.qual 80/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/d89916853f53b8b70da05b25872e30/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html 89/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/e8dc79e6f8dce470fe715c170bd6f4/Sig_18_Blood.deconflicted_germline.FILTER.summary 71/Sig_18_Blood.deconflicted_germline.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/e4/ce338f80f36c887d6250e8884344ae/workflow_summary_mqc.yaml 2/workflow_summary_mqc.yaml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/57ae98b92f6ec6187eb6673a7e27b6/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.count 57/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/f105d8cae3e86a0cb39dd7b9079a38/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.qual 76/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f5b7f0f7da9e730ed7dc1dc53b8347/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff.csv 34/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/818ab2414edd73c0afa13175aae0d8/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.count 52/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/a0ae88cdc258d53789913fccf3efd8/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.qual 73/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/16cb4c798bd5b908222fc9ecd59df6/HCC1395_BL.stats 5/HCC1395_BL.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/b2f93ab4b4da9bf19c37beb0bd7fbc/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html 23/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/a79a42778c19fc661d37f0e78020b6/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.bcftools_stats.txt 43/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/eb0b6704f9b9e7263f926241fe8c0d/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.bcftools_stats.txt 39/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/ae7e4c0dc402c2563301afc3c96f26/Sig_18_Blood_custom.ann_snpEff.csv 21/Sig_18_Blood_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/16c5d963d3504a1b6f6d751bf3d371/variant_qc.json 85/variant_qc.json")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/1b714acbd3deb1c12bb790c5f52f04/HCC1395_BL_custom.ann_snpEff_VEP.ann.summary.html 28/HCC1395_BL_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/202956c18bc741bc3b142a55185eeb/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count 58/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/ef556635cfabb55003e7e128d96e16/Sig_18_Blood.mosdepth.region.dist.txt 9/Sig_18_Blood.mosdepth.region.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/a497e243770dd7dd960401079ce1e7/HCC1395_BL.deconflicted_germline.TsTv.count 60/HCC1395_BL.deconflicted_germline.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/24087b5e8148bf770413f8b7801c7f/Sig_18_tissue.stats 3/Sig_18_tissue.stats")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/0bc4496bfcd8a2d0fa6b5c409b9158/HCC1395_BL.deconflicted_germline.TsTv.qual 84/HCC1395_BL.deconflicted_germline.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/08b6ec675f7fe0c84acc9ae8458542/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html 25/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/10a7511b6894940a509b6c5c3e81f3/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.bcftools_stats.txt 40/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/dfd78915d5fc16f76b75fec4d0d600/HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html 90/HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/e2c637532683780213651e25c65f11/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff.csv 17/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/5cc14b843aeb5ece09f93afb7af022/Sig_18_Blood.TsTv.count 53/Sig_18_Blood.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/452995f79ed4a46284ddaba93068d9/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.qual 79/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/26ef79d3cb1d0e89ace379b84587a5/Sig_18_Blood.deconflicted_germline.bcftools_stats.txt 47/Sig_18_Blood.deconflicted_germline.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/120cac225795b97b282988190e7920/Sig_18_Blood.deconflicted_germline.TsTv.qual 83/Sig_18_Blood.deconflicted_germline.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/b80b63e53edb745e4ed9b7a01b7ac2/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff.csv 87/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/ff3e9bdc117e01ba3edff883771898/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.FILTER.summary 68/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/1e31aeeae5c7a8312d88899a66e9bd/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.qual 75/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/b489e302e23d6c35491c03e3fbb2de/custom_Sig_18_tumor_normal.manta.somatic_sv.FILTER.summary 62/custom_Sig_18_tumor_normal.manta.somatic_sv.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/b8a156109ba4eeae8634e0ee625128/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff.csv 18/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/60d5669f7748781b8be9ce7ea6b9bd/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html 36/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/11/42b2f8ebd110aac75eb876a55b8c46/methods_description_mqc.yaml 1/methods_description_mqc.yaml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/4871fb298b779d647ef3012db89ec6/Sig_18_tissue_vs_Sig_18_Blood.conpair.contamination.txt 16/Sig_18_tissue_vs_Sig_18_Blood.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/039cfc3207d29a2947016789c41ab3/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.FILTER.summary 67/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/f92a32afbbbc4d851cc3c5b1c6b544/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html 26/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/bbebe43081da624132b9c77175c0cd/custom_Sig_18_tumor_normal.strelka.somatic_snvs.FILTER.summary 70/custom_Sig_18_tumor_normal.strelka.somatic_snvs.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/0fe7a63526ebbfb76de04c7be0273a/variant_qc.csv 86/variant_qc.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/2462f5e706fa059a01a9da362fadfb/HCC1395_BL_custom.ann_snpEff.csv 22/HCC1395_BL_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c6442cbb58c733f9d76dad3273dbc/custom_Sig_18_tumor_normal.manta.somatic_sv.bcftools_stats.txt 37/custom_Sig_18_tumor_normal.manta.somatic_sv.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/652987422b525bae6bcc89f42a53f8/HCC1395_BL.deconflicted_germline.bcftools_stats.txt 48/HCC1395_BL.deconflicted_germline.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/f080c928d4109082b6031dd518b3b8/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.count 49/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/9f63b8e53b8a9724142dd69a771ad1/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.qual 82/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/dbfce516f006a5d9292f311a18f2ba/Sig_18_tissue.mosdepth.region.dist.txt 7/Sig_18_tissue.mosdepth.region.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/99a8f59a170719ce35ea54ce1122a2/HCC1395_BL.mosdepth.global.dist.txt 12/HCC1395_BL.mosdepth.global.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/026652b2750720ee328cfd1e3b1dbf/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv 33/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/4aa4a6a951c7e5a618b32b519527fa/Sig_18_Blood.deconflicted_germline.TsTv.count 59/Sig_18_Blood.deconflicted_germline.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/79bb11703c880c12c14f8ea3de6eca/custom_Sig_18_tumor_normal.manta.diploid_sv.bcftools_stats.txt 38/custom_Sig_18_tumor_normal.manta.diploid_sv.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/8d6ee48dda7968775f7d0e7bfbb1da/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html 35/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/9d2ebdc09ea454344befffb2060a44/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.count 50/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b4de810a6f18f26000ab5879536e9a/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.FILTER.summary 64/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/c451220e63e672dbfe7d19f3e5ebda/HCC1395_BL.bcftools_stats.txt 42/HCC1395_BL.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/a31acc98ef376107c98daed45e77db/HCC1395_BL.deconflicted_germline_custom.ann_snpEff.csv 88/HCC1395_BL.deconflicted_germline_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/26b91dd6e78eb906aa1caebb67592a/custom_Sig_18_tumor_normal.strelka.somatic_indels.FILTER.summary 69/custom_Sig_18_tumor_normal.strelka.somatic_indels.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/c1699626b50c157f277dabc2f8f639/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.csv 19/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/4c1b6b591a290179b48fc1ac4724f1/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.count 55/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0afa6caa24e87f82df13515d184af1/HCC1395_tumor.mosdepth.region.dist.txt 13/HCC1395_tumor.mosdepth.region.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/432a0a78baccf0daa4917a914229be/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.csv 29/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/62b211d7a00ca1835990508483246f/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt 45/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0afa6caa24e87f82df13515d184af1/HCC1395_tumor.mosdepth.global.dist.txt 14/HCC1395_tumor.mosdepth.global.dist.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/5ae205eaa2b88f8562c24ea1a74ed1/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.FILTER.summary 63/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/491ef6c5c51094e59d20c1774e845d/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html 31/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/73a92fb4eca6ed410eeef2751f5ace/custom_Sig_18_tumor_normal.manta.diploid_sv.FILTER.summary 61/custom_Sig_18_tumor_normal.manta.diploid_sv.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/9deae44ce86f6f0547a0abd0b6c3e6/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.count 51/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/fc6486a9dedc22b30e424fd5f85c52/Sig_18_Blood_custom.ann_snpEff_VEP.ann.summary.html 27/Sig_18_Blood_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-194ccfaa-d4ea-4fc4-af48-deb22f87deb9/ca/34dea26ea5ff6e39cebeba951a8b3d/multiqc_config.yml multiqc_config.yml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/a9415812f743bb625bc07e6464dc33/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff.csv 20/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/401b3d6bf67198e539149454137a44/HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt 15/HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/982711cb76505f0186e322ea5d350c/HCC1395_BL.deconflicted_germline.FILTER.summary 72/HCC1395_BL.deconflicted_germline.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/052d657ee6e0a6cf167592bd87ab50/Sig_18_Blood.TsTv.qual 77/Sig_18_Blood.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2795358/regression-run/63486558/pipeline_info/nf_core_sarek_software_mqc_versions.yml 91/nf_core_sarek_software_mqc_versions.yml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/2db506627b730e68c0d1efd157990c/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt 46/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/d2274f2c415ede32cc0168335994ca/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.count 56/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.count")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/dc4c1964637351e68d73e6eb3cedb1/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv 30/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/b9902a4a5d42b02602d0c80f3d0940/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html 24/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/7f65e6bd9562b5d01fb8f4c9946679/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html 32/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/8a3a99f58eec87e86afe393d443fe0/HCC1395_BL.FILTER.summary 66/HCC1395_BL.FILTER.summary")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/205b6d048fbeba4a708e35bc52617f/HCC1395_BL.TsTv.qual 78/HCC1395_BL.TsTv.qual")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/9133ba710b70be66a46311393abc6c/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt 44/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (94 inputs)"
echo ""
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d *multiqc_report.html *_data *_plots versions.yml" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300 || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300 || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300 || 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/fe/eea7cffad6ad43857ee9a84a319300/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/73/e7b1d0727a481c85bfc9abce2f6332/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