#!/bin/bash
### ---
### name: 'NFCORE_RNAFUSION:RNAFUSION:MULTIQC'
### container: '292967571998.dkr.ecr.us-west-2.amazonaws.com/biocontainers/multiqc:1.21--pyhdfd78af_0'
### 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 -euo 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 $mem_proc' ERR
/bin/bash -euo pipefail .command.sh &
local task=$!
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/99/e9b6aba0fcb99c588d2f8c8c5fa08f/.exitcode || true
set +u
rm -rf $NXF_SCRATCH || true
exit $exit_status
}
on_term() {
set +e
[[ "$pid" ]] && nxf_kill $pid
}
nxf_launch() {
/bin/bash -euo pipefail .command.run nxf_trace
}
nxf_stage() {
true
# stage input files
downloads=(true)
rm -f 49/rna_s1200_S21_rseqc_extra_mqc.tsv
rm -f 9/rna_s1221_S42.fastp.html
rm -f 37/rna_s1200_S21.junction_annotation.log
rm -f 12/rna_s1221_S42_trimmed_2_fastqc.zip
rm -f 33/rna_s1200_S21.inner_distance_freq.txt
rm -f 4/rna_s1221_S42_2_fastqc.zip
rm -f 24/rna_s1221_S42_collectinsertsize.txt
rm -f 27/rna_s1200_S21.lc_extrap.txt
rm -f 43/rna_s1200_S21.junctionSaturation_plot.r
rm -f 56/rna_s1221_S42_combined_fusions_arriba_visualisation.pdf
rm -f 36/rna_s1221_S42.infer_experiment.txt
rm -f 46/rna_s1221_S42.pos.DupRate.xls
rm -f 52/rna_s1221_S42_seqtool_mqc.tsv
rm -f 50/rna_s1221_S42_rseqc_extra_mqc.tsv
rm -f 25/rna_s1200_S21.attempt1.command.log
rm -f 41/rna_s1200_S21.md.bam.metrics
rm -f 35/rna_s1200_S21.infer_experiment.txt
rm -f 2/workflow_summary_mqc.yaml
rm -f 26/rna_s1221_S42.attempt1.command.log
rm -f 5/rna_s1200_S21_1_fastqc.zip
rm -f 32/rna_s1221_S42_contamination_mqc.tsv
rm -f 51/rna_s1200_S21_seqtool_mqc.tsv
rm -f 30/rna_s1221_S42.bam_stat.txt
rm -f 45/rna_s1200_S21.pos.DupRate.xls
rm -f 19/rna_s1200_S21.Log.final.out
rm -f 13/rna_s1200_S21_trimmed_1_fastqc.zip
rm -f 53/rna_s1200_S21_rna_metrics.txt
rm -f 1/methods_description_mqc.yaml
rm -f .command.run
rm -f 48/rna_s1221_S42_preseq_mqc.tsv
rm -f 34/rna_s1221_S42.inner_distance_freq.txt
rm -f 3/rna_s1221_S42_1_fastqc.zip
rm -f 54/rna_s1221_S42_rna_metrics.txt
rm -f 17/rna_s1221_S42_kallisto_mqc.tsv
rm -f 28/rna_s1221_S42.lc_extrap.txt
rm -f 22/rna_s1221_S42.ReadsPerGene.out.tab
rm -f 16/rna_s1200_S21.log
rm -f 44/rna_s1221_S42.junctionSaturation_plot.r
rm -f .command.sh
rm -f 38/rna_s1221_S42.junction_annotation.log
rm -f 8/rna_s1200_S21.fastp.json
rm -f 11/rna_s1221_S42_trimmed_1_fastqc.zip
rm -f 39/rna_s1200_S21.read_distribution.txt
rm -f 6/rna_s1200_S21_2_fastqc.zip
rm -f 14/rna_s1200_S21_trimmed_2_fastqc.zip
rm -f 20/rna_s1221_S42.Log.final.out
rm -f 57/nf_core_pipeline_software_mqc_versions.yml
rm -f 10/rna_s1200_S21.fastp.html
rm -f 21/rna_s1200_S21.ReadsPerGene.out.tab
rm -f 18/rna_s1200_S21_kallisto_mqc.tsv
rm -f multiqc_config.yml
rm -f 42/rna_s1221_S42.md.bam.metrics
rm -f 40/rna_s1221_S42.read_distribution.txt
rm -f 55/rna_s1200_S21_combined_fusions_arriba_visualisation.pdf
rm -f 47/rna_s1200_S21_preseq_mqc.tsv
rm -f 23/rna_s1200_S21_collectinsertsize.txt
rm -f 15/rna_s1221_S42.log
rm -f 7/rna_s1221_S42.fastp.json
rm -f 29/rna_s1200_S21.bam_stat.txt
rm -f 31/rna_s1200_S21_contamination_mqc.tsv
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/8ec0e2cf090ccaf540c4819e5e447a/rna_s1200_S21_rseqc_extra_mqc.tsv 49/rna_s1200_S21_rseqc_extra_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/c09ea5e5f60184dfc557790011d1e7/rna_s1221_S42.fastp.html 9/rna_s1221_S42.fastp.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/2bf186d6a3d2094148a2c97f707e2d/rna_s1200_S21.junction_annotation.log 37/rna_s1200_S21.junction_annotation.log")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/9842564ab5e6284f20708ae7d540b8/rna_s1221_S42_trimmed_2_fastqc.zip 12/rna_s1221_S42_trimmed_2_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/2ad17fbe025be363aaad2a1ac4a983/rna_s1200_S21.inner_distance_freq.txt 33/rna_s1200_S21.inner_distance_freq.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/47945e98e2188a16dfaa388385f82f/rna_s1221_S42_2_fastqc.zip 4/rna_s1221_S42_2_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/a8b0fc0037f709e46e15e93e19b1b6/rna_s1221_S42_collectinsertsize.txt 24/rna_s1221_S42_collectinsertsize.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/a9dcee53e574961dfa0d2e07640091/rna_s1200_S21.lc_extrap.txt 27/rna_s1200_S21.lc_extrap.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/e693096b5fc513049f8162ace8e09a/rna_s1200_S21.junctionSaturation_plot.r 43/rna_s1200_S21.junctionSaturation_plot.r")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/965e44f324593c920f191b25f67191/rna_s1221_S42_combined_fusions_arriba_visualisation.pdf 56/rna_s1221_S42_combined_fusions_arriba_visualisation.pdf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/ecc3edb662e426a6320b1011c4a29b/rna_s1221_S42.infer_experiment.txt 36/rna_s1221_S42.infer_experiment.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/5cffdfdde0afbf2b9c336c150c0c9b/rna_s1221_S42.pos.DupRate.xls 46/rna_s1221_S42.pos.DupRate.xls")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/505db65cacba6a5ae202225cfd6646/rna_s1221_S42_seqtool_mqc.tsv 52/rna_s1221_S42_seqtool_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/55f6c3866c08b3703d348b1fa1c4ac/rna_s1221_S42_rseqc_extra_mqc.tsv 50/rna_s1221_S42_rseqc_extra_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/a9dcee53e574961dfa0d2e07640091/rna_s1200_S21.attempt1.command.log 25/rna_s1200_S21.attempt1.command.log")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/4db8ffcd3165debb5f9a764e305bfc/rna_s1200_S21.md.bam.metrics 41/rna_s1200_S21.md.bam.metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/95723e02a0de39273502285da91999/rna_s1200_S21.infer_experiment.txt 35/rna_s1200_S21.infer_experiment.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/8d/28923d39bad11e2f80fa6a2462a88d/workflow_summary_mqc.yaml 2/workflow_summary_mqc.yaml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/f40d2a7b90363fc755845b94e6b1c9/rna_s1221_S42.attempt1.command.log 26/rna_s1221_S42.attempt1.command.log")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/4908a8c960393d6cc3003d8a6d5c7d/rna_s1200_S21_1_fastqc.zip 5/rna_s1200_S21_1_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/7ea4622eb11c7f401b994612336cd7/rna_s1221_S42_contamination_mqc.tsv 32/rna_s1221_S42_contamination_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/e88efbea4562445c11d2eca5b1313d/rna_s1200_S21_seqtool_mqc.tsv 51/rna_s1200_S21_seqtool_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/d9473ba92378e08546dc8ba87b7cfe/rna_s1221_S42.bam_stat.txt 30/rna_s1221_S42.bam_stat.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e21a3393f704bd437cee124b9caf35/rna_s1200_S21.pos.DupRate.xls 45/rna_s1200_S21.pos.DupRate.xls")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/9b890cf91cfb3ad2b45c245b88967b/rna_s1200_S21.Log.final.out 19/rna_s1200_S21.Log.final.out")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/1ea93249256fe4a39cde8b04f853b6/rna_s1200_S21_trimmed_1_fastqc.zip 13/rna_s1200_S21_trimmed_1_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/9c1a12c6c75205180fd80d5e6a265b/rna_s1200_S21_rna_metrics.txt 53/rna_s1200_S21_rna_metrics.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/68/ad7341a39d5ad43dc0cca82aefa42a/methods_description_mqc.yaml 1/methods_description_mqc.yaml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/e9b6aba0fcb99c588d2f8c8c5fa08f/.command.run .command.run")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/79007fdcb5beda13eb32f4b7ab6288/rna_s1221_S42_preseq_mqc.tsv 48/rna_s1221_S42_preseq_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/57d30df15f462531526ca79751a889/rna_s1221_S42.inner_distance_freq.txt 34/rna_s1221_S42.inner_distance_freq.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/47945e98e2188a16dfaa388385f82f/rna_s1221_S42_1_fastqc.zip 3/rna_s1221_S42_1_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/3d3ddb375a39fc4754be40a98f17cb/rna_s1221_S42_rna_metrics.txt 54/rna_s1221_S42_rna_metrics.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/6b3bfada533b37a219de86fb4854d0/rna_s1221_S42_kallisto_mqc.tsv 17/rna_s1221_S42_kallisto_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/f40d2a7b90363fc755845b94e6b1c9/rna_s1221_S42.lc_extrap.txt 28/rna_s1221_S42.lc_extrap.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b225bc5b1ba78c82b255ecb9cbed55/rna_s1221_S42.ReadsPerGene.out.tab 22/rna_s1221_S42.ReadsPerGene.out.tab")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/4387bc227c1404a9487ab1e2100ef0/rna_s1200_S21.log 16/rna_s1200_S21.log")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/266398dcbede229f5c77fb60bbcdb3/rna_s1221_S42.junctionSaturation_plot.r 44/rna_s1221_S42.junctionSaturation_plot.r")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/e9b6aba0fcb99c588d2f8c8c5fa08f/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/4e707c9d85003033e3cee908e79145/rna_s1221_S42.junction_annotation.log 38/rna_s1221_S42.junction_annotation.log")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/d04b94a28790f752b68b09b6b7ea9f/rna_s1200_S21.fastp.json 8/rna_s1200_S21.fastp.json")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/9842564ab5e6284f20708ae7d540b8/rna_s1221_S42_trimmed_1_fastqc.zip 11/rna_s1221_S42_trimmed_1_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/4073c413a42a440b737eabe597721c/rna_s1200_S21.read_distribution.txt 39/rna_s1200_S21.read_distribution.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/4908a8c960393d6cc3003d8a6d5c7d/rna_s1200_S21_2_fastqc.zip 6/rna_s1200_S21_2_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/1ea93249256fe4a39cde8b04f853b6/rna_s1200_S21_trimmed_2_fastqc.zip 14/rna_s1200_S21_trimmed_2_fastqc.zip")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b225bc5b1ba78c82b255ecb9cbed55/rna_s1221_S42.Log.final.out 20/rna_s1221_S42.Log.final.out")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-s3-gitlab-results/rnafusion/build2776425/baseline-run/62916108/pipeline_info/nf_core_pipeline_software_mqc_versions.yml 57/nf_core_pipeline_software_mqc_versions.yml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/d04b94a28790f752b68b09b6b7ea9f/rna_s1200_S21.fastp.html 10/rna_s1200_S21.fastp.html")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/9b890cf91cfb3ad2b45c245b88967b/rna_s1200_S21.ReadsPerGene.out.tab 21/rna_s1200_S21.ReadsPerGene.out.tab")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/c0df1d3d8b77e0e37d2675487ecab0/rna_s1200_S21_kallisto_mqc.tsv 18/rna_s1200_S21_kallisto_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-b08e5fb2-6d8b-4618-9fdd-da85b61f0360/d4/e5bc4be8b166e7b115663559569cbe/multiqc_config.yml multiqc_config.yml")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/9eec10ce28ffd340977b2784449139/rna_s1221_S42.md.bam.metrics 42/rna_s1221_S42.md.bam.metrics")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/7988c3f4dcf043f9b885c53a89fd82/rna_s1221_S42.read_distribution.txt 40/rna_s1221_S42.read_distribution.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/8fce3d0c1f643fc992a6548d66d66c/rna_s1200_S21_combined_fusions_arriba_visualisation.pdf 55/rna_s1200_S21_combined_fusions_arriba_visualisation.pdf")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/39f41e09e7fe8298c17fbbec28916e/rna_s1200_S21_preseq_mqc.tsv 47/rna_s1200_S21_preseq_mqc.tsv")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/60f010e4833ef3867d8b691ae98ed2/rna_s1200_S21_collectinsertsize.txt 23/rna_s1200_S21_collectinsertsize.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/89083a6b6c26ad0436dea9e1e5dd89/rna_s1221_S42.log 15/rna_s1221_S42.log")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/c09ea5e5f60184dfc557790011d1e7/rna_s1221_S42.fastp.json 7/rna_s1221_S42.fastp.json")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/aa98b3cfa3b0ba20bdebd73706c1ee/rna_s1200_S21.bam_stat.txt 29/rna_s1200_S21.bam_stat.txt")
downloads+=("nxf_s3_download s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/9ffa0e45c616ff3c75c07e5dc46dec/rna_s1200_S21_contamination_mqc.tsv 31/rna_s1200_S21_contamination_mqc.tsv")
nxf_parallel "${downloads[@]}"
echo "==> STAGING COMPLETE (60 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/99/e9b6aba0fcb99c588d2f8c8c5fa08f")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/e9b6aba0fcb99c588d2f8c8c5fa08f || true
nxf_s3_upload .command.err s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/e9b6aba0fcb99c588d2f8c8c5fa08f || true
nxf_s3_upload .command.trace s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/e9b6aba0fcb99c588d2f8c8c5fa08f || 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/99/e9b6aba0fcb99c588d2f8c8c5fa08f/.command.begin
set +u
set -u
/opt/s5cmd/bin/s5cmd --log error cp "s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/ce/16629576e63588da45f5d6981b665f/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