#!/bin/bash
#SBATCH --dependency=afterany:11790:11791
set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p6000/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56/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 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']] = '60'
param[['scratch']] = '100'
param[['partition']] = 'course'
param[['process_mode']] = 'DATASET'
param[['samples']] = 'Undifferentiated_lung_cells,Differentiated_lung_cells'
param[['node']] = ''
param[['name']] = 'SCReportMultipleSamplesSeurat'
param[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30'
param[['refFeatureFile']] = 'genes.gtf'
param[['tissue']] = 'Airway epithelium'
param[['enrichrDatabase']] = 'Azimuth_Cell_Types_2021,PanglaoDB_Augmented_2021'
param[['SingleR']] = 'none'
param[['pcGenes']] = ''
param[['npcs']] = '30'
param[['resolution']] = '0.6'
param[['SCT.regress.CellCycle']] = 'false'
param[['DE.method']] = 'wilcox'
param[['DE.regress']] = ''
param[['min.pct']] = '0.1'
param[['logfc.threshold']] = '0.25'
param[['integrationMethod']] = 'CCA'
param[['additionalFactors']] = ''
param[['STACASAnnotationFile']] = ''
param[['computePathwayTFActivity']] = 'false'
param[['specialOptions']] = ''
param[['mail']] = 'lopitz@fgcz.ethz.ch'
param[['sushi_app']] = 'ScSeuratCombineApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p6000/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'SCReportMultipleSamplesSeurat'
output[['Species']] = 'Homo sapiens (human)'
output[['Static Report [Link]']] = 'p6000/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56/SCReportMultipleSamplesSeurat/00index.html'
output[['Report [File]']] = 'p6000/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56/SCReportMultipleSamplesSeurat'
output[['Order Id [B-Fabric]']] = '5495,5444'
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p6000/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56/input_dataset.tsv'
EzAppScSeuratCombine\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r SCReportMultipleSamplesSeurat /srv/GT/analysis/course_sushi/public/gstore/projects/p6000/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56/
cd /scratch
rm -rf /scratch/o5495_o5444_ScSeuratCombine_CCA_2024-12-06--17-30-56_temp$$ || exit 1


echo __SCRIPT END__