#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Excerpt_2025-07-24--16-39-45/scripts/Count_mut22_ventricles_100k_1.sh
set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/o35755_Excerpt_2025-07-24--16-39-45_mut22_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Excerpt_2025-07-24--16-39-45/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


#### NOW THE ACTUAL JOBS STARTS
module load Tools/exceRpt/5.0.0
module load Aligner/STAR/2.6.1e
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']] = '8'
param[['ram']] = '30'
param[['scratch']] = '100'
param[['partition']] = 'user'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'mut11,mut22'
param[['refBuild']] = 'Homo_sapiens/UCSC/hg38'
param[['ENDOGENOUS_LIB_PRIORITY']] = 'miRNA,tRNA,piRNA,gencode,circRNA'
param[['TRIM_N_BASES_5p']] = '0'
param[['TRIM_N_BASES_3p']] = '0'
param[['MIN_READ_LENGTH']] = '18'
param[['QFILTER_MIN_QUAL']] = '20'
param[['QFILTER_MIN_READ_FRAC']] = '80'
param[['RANDOM_BARCODE_LENGTH']] = '0'
param[['RANDOM_BARCODE_LOCATION']] = '-5p -3p'
param[['KEEP_RANDOM_BARCODE_STATS']] = 'false'
param[['STAR_alignEndsType']] = 'Local'
param[['STAR_outFilterMatchNmin']] = '18'
param[['STAR_outFilterMatchNminOverLread']] = '0.9'
param[['STAR_outFilterMismatchNmax']] = '1'
param[['REMOVE_LARGE_INTERMEDIATE_FILES']] = 'true'
param[['cmdOptions']] = 'JAVA_RAM=10G'
param[['mail']] = ''
param[['ExcerptVersion']] = 'Tools/exceRpt/5.0.0'
param[['starVersion']] = 'Aligner/STAR/2.6.1e'
param[['sushi_app']] = 'ExceRptApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/o35755_Excerpt_2025-07-24--16-39-45'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'mut22'
output[['excerpt [File]']] = 'p1001/o35755_Excerpt_2025-07-24--16-39-45/mut22'
output[['Species']] = 'Mus musculus'
output[['refBuild']] = 'Homo_sapiens/UCSC/hg38'
output[['Genotype [Factor]']] = 'mut'
output[['BFabric Info [B-Fabric]']] = 'test2'
output[['Order Id [B-Fabric]']] = '35755'
input = list()
input[['Name']] = 'mut22'
input[['Read1']] = 'p1001/ventricles_100k/MutantSample_2_R1.fastq.gz'
input[['Read2']] = 'p1001/ventricles_100k/MutantSample_2_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']] = 'test2'
input[['Order Id']] = '35755'
EzAppExceRpt\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r mut22 /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Excerpt_2025-07-24--16-39-45/
cd /scratch
rm -rf /scratch/o35755_Excerpt_2025-07-24--16-39-45_mut22_temp$$ || exit 1