#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/Bowtie2_2024-11-01--10-14-56_NA12891_chr10_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1010/Bowtie2_2024-11-01--10-14-56/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 Tools/samtools/1.20 Aligner/Bowtie2/2.5.4 QC/fastp/0.23.4 Dev/R/4.4.0 Tools/Picard/3.2.0

#### 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']] = '8'
param[['ram']] = '30'
param[['scratch']] = '200'
param[['partition']] = 'course'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'NA12878_chr10,NA12889_chr10,NA12890_chr10,NA12891_chr10,NA12892_chr10'
param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh37.p13/Annotation/Version-2015-03-05'
param[['paired']] = 'true'
param[['secondRef']] = ''
param[['cmdOptions']] = '--no-mixed --no-discordant --very-sensitive -X 1000'
param[['trimAdapter']] = 'true'
param[['trim_front1']] = '0'
param[['trim_tail1']] = '0'
param[['cut_front']] = 'true'
param[['cut_front_window_size']] = '4'
param[['cut_front_mean_quality']] = '20'
param[['cut_tail']] = 'true'
param[['cut_tail_window_size']] = '4'
param[['cut_tail_mean_quality']] = '20'
param[['cut_right']] = 'true'
param[['cut_right_window_size']] = '4'
param[['cut_right_mean_quality']] = '20'
param[['average_qual']] = '20'
param[['max_len1']] = '0'
param[['max_len2']] = '0'
param[['poly_x_min_len']] = '10'
param[['length_required']] = '18'
param[['cmdOptionsFastp']] = ''
param[['markDuplicates']] = 'true'
param[['generateBigWig']] = 'false'
param[['specialOptions']] = ''
param[['mail']] = ''
param[['sushi_app']] = 'Bowtie2App'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1010/Bowtie2_2024-11-01--10-14-56'
param[['isLastJob']] = FALSE
output = list()
output[['Name']] = 'NA12891_chr10'
output[['BAM [File]']] = 'p1010/Bowtie2_2024-11-01--10-14-56/NA12891_chr10.bam'
output[['BAI [File]']] = 'p1010/Bowtie2_2024-11-01--10-14-56/NA12891_chr10.bam.bai'
output[['IGV [Link]']] = 'p1010/Bowtie2_2024-11-01--10-14-56/NA12891_chr10-igv.html'
output[['Species']] = 'Homo sapien'
output[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh37.p13/Annotation/Version-2015-03-05'
output[['paired']] = 'true'
output[['Read Count']] = '250000'
output[['IGV [File]']] = 'p1010/Bowtie2_2024-11-01--10-14-56/NA12891_chr10-igv.html'
output[['PreprocessingLog [File]']] = 'p1010/Bowtie2_2024-11-01--10-14-56/NA12891_chr10_preprocessing.log'
output[['Bowtie2Log [File]']] = 'p1010/Bowtie2_2024-11-01--10-14-56/NA12891_chr10_bowtie2.log'
input = list()
input[['Name']] = 'NA12891_chr10'
input[['Read1']] = 'p1000/chr10_WES_reads_subSampled/NA12891_chr10_R1.fastq.gz'
input[['Read2']] = 'p1000/chr10_WES_reads_subSampled/NA12891_chr10_R2.fastq.gz'
input[['Adapter1']] = 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
input[['Adapter2']] = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
input[['strandMode']] = 'both'
input[['Species']] = 'Homo sapien'
input[['Read Count']] = '250000'
EzAppBowtie2\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r NA12891_chr10.bam /srv/GT/analysis/course_sushi/public/gstore/projects/p1010/Bowtie2_2024-11-01--10-14-56/
rsync -r NA12891_chr10.bam.bai /srv/GT/analysis/course_sushi/public/gstore/projects/p1010/Bowtie2_2024-11-01--10-14-56/
rsync -r NA12891_chr10-igv.html /srv/GT/analysis/course_sushi/public/gstore/projects/p1010/Bowtie2_2024-11-01--10-14-56/
rsync -r NA12891_chr10_preprocessing.log /srv/GT/analysis/course_sushi/public/gstore/projects/p1010/Bowtie2_2024-11-01--10-14-56/
rsync -r NA12891_chr10_bowtie2.log /srv/GT/analysis/course_sushi/public/gstore/projects/p1010/Bowtie2_2024-11-01--10-14-56/
cd /scratch
rm -rf /scratch/Bowtie2_2024-11-01--10-14-56_NA12891_chr10_temp$$ || exit 1


echo __SCRIPT END__