#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/Kraken_2024-12-13--09-46-12_sample1_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p8004/Kraken_2024-12-13--09-46-12/input_dataset.tsv
LAST_JOB=FALSE
echo "Job runs on `hostname`"
echo "at $SCRATCH_DIR"
mkdir $SCRATCH_DIR || exit 1
cd $SCRATCH_DIR || exit 1
source /usr/local/ngseq/etc/lmod_profile
module add QC/fastp/0.23.4 Dev/R/4.4.0 Tools/kraken/2.1.3 Tools/Krona/2.8.1

#### NOW THE ACTUAL JOBS STARTS
R --vanilla --slave<<  EOT
EZ_GLOBAL_VARIABLES <<- '/usr/local/ngseq/opt/EZ_GLOBAL_VARIABLES.txt'
if (!library(ezRun, logical.return = TRUE)){
message('retry loading ezRun')
Sys.sleep(120)
library(ezRun)
}
param = list()
param[['cores']] = '4'
param[['ram']] = '15'
param[['scratch']] = '30'
param[['partition']] = 'course'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'sample1,sample2'
param[['paired']] = 'false'
param[['krakenDBOpt']] = 'bacteria'
param[['krakenConfidenceOpt']] = '0.0'
param[['krakenPhredOpt']] = '0'
param[['cmdOptions']] = ''
param[['trimAdapter']] = 'true'
param[['trim_front1']] = '0'
param[['trim_tail1']] = '0'
param[['cut_front']] = 'false'
param[['cut_front_window_size']] = '4'
param[['cut_front_mean_quality']] = '20'
param[['cut_tail']] = 'false'
param[['cut_tail_window_size']] = '4'
param[['cut_tail_mean_quality']] = '20'
param[['cut_right']] = 'false'
param[['cut_right_window_size']] = '4'
param[['cut_right_mean_quality']] = '20'
param[['average_qual']] = '0'
param[['max_len1']] = '0'
param[['max_len2']] = '0'
param[['poly_x_min_len']] = '10'
param[['length_required']] = '18'
param[['cmdOptionsFastp']] = ''
param[['markDuplicates']] = 'true'
param[['mail']] = ''
param[['sushi_app']] = 'KrakenApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p8004/Kraken_2024-12-13--09-46-12'
param[['isLastJob']] = FALSE
output = list()
output[['Name']] = 'sample1'
output[['KronaReport [Link]']] = 'p8004/Kraken_2024-12-13--09-46-12/sample1.html'
output[['KrakenOut [File]']] = 'p8004/Kraken_2024-12-13--09-46-12/sample1.txt'
output[['KrakenReport [File]']] = 'p8004/Kraken_2024-12-13--09-46-12/sample1.report.txt'
output[['KronaOutDir [File]']] = 'p8004/Kraken_2024-12-13--09-46-12/sample1.html.files'
output[['KronaOut [File]']] = 'p8004/Kraken_2024-12-13--09-46-12/sample1.html'
input = list()
input[['Name']] = 'sample1'
input[['Read1']] = 'p6000/MetaAtlas_data/sample1_R1.fastq.gz'
input[['Read2']] = 'p6000/MetaAtlas_data/sample1_R2.fastq.gz'
EzAppKraken\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r sample1.txt /srv/GT/analysis/course_sushi/public/gstore/projects/p8004/Kraken_2024-12-13--09-46-12/
rsync -r sample1.report.txt /srv/GT/analysis/course_sushi/public/gstore/projects/p8004/Kraken_2024-12-13--09-46-12/
rsync -r sample1.html.files /srv/GT/analysis/course_sushi/public/gstore/projects/p8004/Kraken_2024-12-13--09-46-12/
rsync -r sample1.html /srv/GT/analysis/course_sushi/public/gstore/projects/p8004/Kraken_2024-12-13--09-46-12/
cd /scratch
rm -rf /scratch/Kraken_2024-12-13--09-46-12_sample1_temp$$ || exit 1


echo __SCRIPT END__