#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/scripts/Map_S1_undiff_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh
set -eux
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/STAR_2025-11-25--15-44-24_S1_undiff_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/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 Aligner/STAR/2.7.11b Tools/samtools/1.20 Dev/jdk/21 Dev/R/4.5.0 Dev/Python/3.12.8 Tools/Picard/3.2.0 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']] = '8'
param[['ram']] = '30'
param[['scratch']] = '100'
param[['partition']] = 'course'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff'
param[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03'
param[['paired']] = 'false'
param[['strandMode']] = 'antisense'
param[['refFeatureFile']] = 'genes.gtf'
param[['secondRef']] = ''
param[['cmdOptions']] = '--sjdbOverhang 150 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 100000 --alignMatesGapMax 100000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 10 ConcordantPair --outSAMmultNmax 4'
param[['getJunctions']] = 'false'
param[['twopassMode']] = 'false'
param[['trimAdapter']] = 'true'
param[['trim_front1']] = '4'
param[['trim_tail1']] = '0'
param[['cut_front']] = 'false'
param[['cut_front_window_size']] = '4'
param[['cut_front_mean_quality']] = '20'
param[['cut_tail']] = 'false'
param[['cut_tail_window_size']] = '4'
param[['cut_tail_mean_quality']] = '20'
param[['cut_right']] = 'false'
param[['cut_right_window_size']] = '4'
param[['cut_right_mean_quality']] = '20'
param[['average_qual']] = '0'
param[['max_len1']] = '0'
param[['max_len2']] = '0'
param[['poly_x_min_len']] = '10'
param[['length_required']] = '18'
param[['cmdOptionsFastp']] = ''
param[['barcodePattern']] = ''
param[['markDuplicates']] = 'false'
param[['specialOptions']] = ''
param[['mail']] = ''
param[['sushi_app']] = 'STARApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/STAR_2025-11-25--15-44-24'
param[['isLastJob']] = FALSE
output = list()
output[['Name']] = 'S1_undiff'
output[['BAM [File]']] = 'p1001/STAR_2025-11-25--15-44-24/S1_undiff.bam'
output[['BAI [File]']] = 'p1001/STAR_2025-11-25--15-44-24/S1_undiff.bam.bai'
output[['IGV [Link,File]']] = 'p1001/STAR_2025-11-25--15-44-24/S1_undiff-igv.html'
output[['Species']] = 'Homo sapiens (human)'
output[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03'
output[['paired']] = 'false'
output[['refFeatureFile']] = 'genes.gtf'
output[['strandMode']] = 'antisense'
output[['Read Count']] = '100000'
output[['PreprocessingLog [File]']] = 'p1001/STAR_2025-11-25--15-44-24/S1_undiff_preprocessing.log'
output[['STARLog [File]']] = 'p1001/STAR_2025-11-25--15-44-24/S1_undiff_STAR.log'
output[['Condition [Factor]']] = 'undiff'
output[['Tube [Characteristic]']] = 'p3009_5638/7'
output[['InputAmount [Characteristic]']] = '100'
grandchild_output = list()
input = list()
input[['Name']] = 'S1_undiff'
input[['Read1']] = 'p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S1a_undiff_R1-subsample.fastq.gz'
input[['Species']] = 'Homo sapiens (human)'
input[['Tube']] = 'p3009_5638/7'
input[['Condition']] = 'undiff'
input[['Adapter1']] = 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
input[['strandMode']] = 'antisense'
input[['LibraryPrepKit']] = 'Lexogen_mRNA_stranded'
input[['EnrichmentMethod']] = 'PolyA_mRNA_Lexogen_stranded'
input[['InputAmount']] = '100'
input[['Read Count']] = '100000'
input[['Treatment (Factor)']] = ''
EzAppSTAR\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r S1_undiff.bam /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/
rsync -r S1_undiff.bam.bai /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/
rsync -r S1_undiff-igv.html /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/
rsync -r S1_undiff_preprocessing.log /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/
rsync -r S1_undiff_STAR.log /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/
cd /scratch
rm -rf /scratch/STAR_2025-11-25--15-44-24_S1_undiff_temp$$ || exit 1