#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/o5495_o5444_ScSeurat_2024-12-05--10-06-08_Differentiated_lung_cells_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p6013/o5495_o5444_ScSeurat_2024-12-05--10-06-08/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']] = '4'
param[['ram']] = '30'
param[['scratch']] = '30'
param[['partition']] = 'course'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'Undifferentiated_lung_cells,Differentiated_lung_cells'
param[['name']] = 'ScSeurat'
param[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30'
param[['refFeatureFile']] = 'genes.gtf'
param[['geneCountModel']] = ''
param[['SCT.regress.CellCycle']] = 'false'
param[['DE.method']] = 'wilcox'
param[['min.pct']] = '0.1'
param[['min.diff.pct']] = '0.1'
param[['pvalue_allMarkers']] = '0.01'
param[['logfc.threshold']] = '0.25'
param[['tissue']] = 'Human Lung'
param[['enrichrDatabase']] = 'Azimuth_Cell_Types_2021'
param[['Azimuth']] = 'lungref'
param[['SingleR']] = 'HumanPrimaryCellAtlasData'
param[['cellxgeneUrl']] = ''
param[['cellxgeneLabel']] = ''
param[['npcs']] = '20'
param[['pcGenes']] = ''
param[['resolution']] = '0.6'
param[['nreads']] = ''
param[['ngenes']] = ''
param[['perc_mito']] = ''
param[['perc_riboprot']] = '70'
param[['cellsFraction']] = '0.0001'
param[['nUMIs']] = '1'
param[['filterByExpression']] = ''
param[['estimateAmbient']] = 'true'
param[['computePathwayTFActivity']] = 'false'
param[['specialOptions']] = ''
param[['mail']] = ''
param[['sushi_app']] = 'ScSeuratApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p6013/o5495_o5444_ScSeurat_2024-12-05--10-06-08'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'Differentiated_lung_cells'
output[['Species']] = 'Homo sapiens (human)'
output[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30'
output[['refFeatureFile']] = 'genes.gtf'
output[['Static Report [Link]']] = 'p6013/o5495_o5444_ScSeurat_2024-12-05--10-06-08/Differentiated_lung_cells_SCReport/00index.html'
output[['SC Cluster Report [File]']] = 'p6013/o5495_o5444_ScSeurat_2024-12-05--10-06-08/Differentiated_lung_cells_SCReport'
output[['SC Seurat']] = 'p6013/o5495_o5444_ScSeurat_2024-12-05--10-06-08/Differentiated_lung_cells_SCReport/scData.qs'
output[['Condition [Factor]']] = 'Differentiated'
output[['Sample Id [B-Fabric]']] = 'bfs_193577'
output[['Order Id [B-Fabric]']] = '5444'
input = list()
input[['Name']] = 'Differentiated_lung_cells'
input[['Species']] = 'Homo sapiens (human)'
input[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30'
input[['refFeatureFile']] = 'genes.gtf'
input[['featureLevel']] = 'gene'
input[['transcriptTypes']] = 'protein_coding,rRNA,tRNA,Mt_rRNA,Mt_tRNA'
input[['SCDataOrigin']] = '10X'
input[['ResultDir']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Differentiated_lung_cells'
input[['Report']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Differentiated_lung_cells/web_summary.html'
input[['CountMatrix']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Differentiated_lung_cells/filtered_feature_bc_matrix'
input[['UnfilteredCountMatrix']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Differentiated_lung_cells/raw_feature_bc_matrix'
input[['Read Count']] = '329724344'
input[['Condition']] = 'Differentiated'
input[['Sample Id']] = 'bfs_193577'
input[['Order Id']] = '5444'
EzAppScSeurat\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r Differentiated_lung_cells_SCReport /srv/GT/analysis/course_sushi/public/gstore/projects/p6013/o5495_o5444_ScSeurat_2024-12-05--10-06-08/
cd /scratch
rm -rf /scratch/o5495_o5444_ScSeurat_2024-12-05--10-06-08_Differentiated_lung_cells_temp$$ || exit 1


echo __SCRIPT END__