#!/bin/bash
#SBATCH --dependency=afterany:3723:3724:3725:3726:3727
set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/samtoolsmpileup_single_HB_2024-11-01--13-16-26_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/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 Tools/samtools/1.20 Tools/bcftools/1.20 Dev/jdk/21 Tools/Picard/3.2.0 Dev/R/4.4.0

#### 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']] = '100'
param[['partition']] = 'course'
param[['process_mode']] = 'DATASET'
param[['samples']] = 'NA12878_chr10'
param[['paired']] = 'true'
param[['name']] = 'Mpileup_Variants'
param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh37.p13/Annotation/Version-2015-03-05'
param[['region']] = ''
param[['mpileupOptions']] = '--skip-indels --annotate AD,INFO/AD,ADF,ADR,SP'
param[['callOptions']] = '--multiallelic-caller --keep-alts --variants-only'
param[['filterOptions']] = '--include "MIN(DP)>5"'
param[['specialOptions']] = ''
param[['mail']] = ''
param[['sushi_app']] = 'MpileupApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'Mpileup_Variants'
output[['VCF [File]']] = 'p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/Mpileup_Variants.vcf.gz'
output[['TBI [File]']] = 'p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/Mpileup_Variants.vcf.gz.tbi'
output[['Report [File]']] = 'p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/Mpileup_Variants'
output[['Html [Link]']] = 'p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/Mpileup_Variants/00index.html'
output[['Species']] = 'Homo sapien'
output[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh37.p13/Annotation/Version-2015-03-05'
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/input_dataset.tsv'
EzAppMpileup\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r Mpileup_Variants.vcf.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/
rsync -r Mpileup_Variants.vcf.gz.tbi /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/
rsync -r Mpileup_Variants /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/samtoolsmpileup_single_HB_2024-11-01--13-16-26/
cd /scratch
rm -rf /scratch/samtoolsmpileup_single_HB_2024-11-01--13-16-26_temp$$ || exit 1


echo __SCRIPT END__