#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/test_masa2_2024-11-15--10-34-02_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/test_masa2_2024-11-15--10-34-02/input_dataset.tsv
LAST_JOB=TRUE
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/FastQC/0.12.1 Dev/R/4.4.0 Tools/Picard/3.2.0 Tools/samtools/1.20 Dev/Python/3.11.5 QC/fastp/0.23.4

#### 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']] = '1'
param[['ram']] = '15'
param[['scratch']] = '10'
param[['partition']] = 'user'
param[['process_mode']] = 'DATASET'
param[['samples']] = 'mut11,mut22'
param[['paired']] = 'true'
param[['showNativeReports']] = 'false'
param[['specialOptions']] = ''
param[['cmdOptions']] = ''
param[['mail']] = 'masaomi.hatakeyama@uzh.ch'
param[['sushi_app']] = 'FastqcApp'
param[['name']] = 'FastQC'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/test_masa2_2024-11-15--10-34-02'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'FastQC'
output[['MultiQC Report [Link]']] = 'p1001/test_masa2_2024-11-15--10-34-02/multi_FastQC/multiqc_report.html'
output[['MultiQC [File]']] = 'p1001/test_masa2_2024-11-15--10-34-02/multi_FastQC'
output[['FastQC [File]']] = 'p1001/test_masa2_2024-11-15--10-34-02/FastQC'
output[['Order Id [B-Fabric]']] = '35755'
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/test_masa2_2024-11-15--10-34-02/input_dataset.tsv'
EzAppFastqc\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r multi_FastQC /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/test_masa2_2024-11-15--10-34-02/
rsync -r FastQC /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/test_masa2_2024-11-15--10-34-02/
cd /scratch
rm -rf /scratch/test_masa2_2024-11-15--10-34-02_temp$$ || exit 1


echo __SCRIPT END__