#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/scripts/QC_mut11_ventricles_100k_1.sh
set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/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 Dev/jdk/21

#### NOW THE ACTUAL JOBS STARTS
. '/usr/local/ngseq/miniforge3/etc/profile.d/conda.sh'
conda activate gi_atac-seq-pipeline
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']] = '16'
param[['ram']] = '40'
param[['scratch']] = '200'
param[['partition']] = 'user'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'mut11,mut22'
param[['paired']] = 'true'
param[['nReads']] = '25000000'
param[['name']] = 'AtacENCODE'
param[['cmdOptions']] = ''
param[['mail']] = ''
param[['sushi_app']] = 'AtacENCODEApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/o35755_AtacENCODE_2025-07-24--16-43-39'
param[['isLastJob']] = FALSE
output = list()
output[['Name']] = 'mut11'
output[['Report [File]']] = 'p1001/o35755_AtacENCODE_2025-07-24--16-43-39/mut11_qc.html'
output[['Stats [File]']] = 'p1001/o35755_AtacENCODE_2025-07-24--16-43-39/mut11_qc.json'
output[['Html [Link]']] = 'p1001/o35755_AtacENCODE_2025-07-24--16-43-39/mut11_qc.html'
input = list()
input[['Name']] = 'mut11'
input[['Read1']] = 'p1001/ventricles_100k/MutantSample_1_R1.fastq.gz'
input[['Read2']] = 'p1001/ventricles_100k/MutantSample_1_R2.fastq.gz'
input[['Species']] = 'Mus musculus'
input[['Adapter1']] = 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
input[['Adapter2']] = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
input[['StrandMode']] = 'both'
input[['Enrichment Kit']] = 'poly-A'
input[['Read Count']] = '100000'
input[['Genotype']] = 'mut'
input[['BFabric Info']] = 'test1'
input[['Order Id']] = '35755'
EzAppAtacENCODE\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r mut11_qc.html /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/
rsync -r mut11_qc.json /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_AtacENCODE_2025-07-24--16-43-39/
cd /scratch
rm -rf /scratch/o35755_AtacENCODE_2025-07-24--16-43-39_mut11_temp$$ || exit 1