#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/o5495_o5444_ScSeurat_2024-12-05--09-59-39_Undifferentiated_lung_cells_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p6007/o5495_o5444_ScSeurat_2024-12-05--09-59-39/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 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 Abdomen,Human Adipose tissue,Human Adrenal gland,Human Adventitia,Human Airway,Human Airway epithelium,Human Amniotic fluid,Human Artery,Human Arthrosis,Human Articular Cartilage,Human Articulation,Human Ascites,Human Belly,Human Bile duct,Human Biliary tract,Human Bladder,Human Blood,Human Blood vessel,Human Bone,Human Bone marrow,Human Brain,Human Breast,Human Bronchi,Human Bronchus,Human Cartilage,Human Cavernosum,Human Cerebral organoid,Human Cervix,Human Colon,Human Cornea,Human Decidua,Human Embryo,Human Endocrine organ,Human Endometrium,Human Epidermis,Human Epithelium,Human Esophageal,Human Esophagus,Human Eye,Human Fetal brain,Human Fetal liver,Human Fetal striatum,Human Fetus,Human Fundic gland,Human Gall bladder,Human Gastrointestinal tract,Human Genitals,Human Germ,Human Gingiva,Human Gonad,Human Gut,Human Head,Human Head and neck,Human Heart,Human Inferior colliculus,Human Intervertebral disc,Human Intestine,Human Joint,Human Kidney,Human Knee,Human Knee joint,Human Larynx,Human Ligament,Human Limb,Human Liver,Human Lung,Human Lymph,Human Lymph node,Human Lymphoid tissue,Human Mammary gland,Human Meniscus,Human Muscle,Human Nasal,Human Nasopharynx,Human Neck,Human Nerve,Human Nodular tissue,Human Nose,Human Oral cavity,Human Ovary,Human Oviduct,Human Palatine tonsil,Human Pancreas,Human Periodontium,Human Periosteum,Human Peritoneal fluid,Human Peritoneum,Human Pharynx,Human Placenta,Human Pleura,Human Prostate,Human Respiratory tract,Human Salivary gland,Human Scalp,Human Sinus tissue,Human Skeletal muscle,Human Skin,Human Soft tissue,Human Spinal cord,Human Spleen,Human Sputum,Human Stomach,Human Suprarenal gland,Human Synovial,Human Synovial fluid,Human Synovium,Human Taste bud,Human Tendon,Human Testis,Human Thorax,Human Thymus,Human Thyroid,Human Tongue,Human Tonsil,Human Tooth,Human Trachea,Human Umbilical cord,Human Undefined,Human Urine,Human Uterine cervix,Human Uterus,Human Vagina,Human Vein,Mouse Abdomen,Mouse Adipose tissue,Mouse Anorectal junction,Mouse Aorta,Mouse Arm,Mouse Artery,Mouse Belly,Mouse Bladder,Mouse Blood,Mouse Blood vessel,Mouse Bone,Mouse Bone marrow,Mouse Brain,Mouse Breast,Mouse Cartilage,Mouse Cerebellum,Mouse Colon,Mouse Connective tissue,Mouse Dorsal root ganglia,Mouse Ear,Mouse Embryo,Mouse Embryos,Mouse Endocardium,Mouse Endometrium,Mouse Epithelium,Mouse Esophagus,Mouse Eye,Mouse Fetal brain,Mouse Fetal heart,Mouse Flesh,Mouse Foot,Mouse Gastrointestinal tract,Mouse Gingiva,Mouse Gut,Mouse Heart,Mouse Hind limb,Mouse Hindlimb,Mouse Intestine,Mouse Intestine/Proliferating ECs pool,Mouse Kidney,Mouse Knee,Mouse Limb,Mouse Liver,Mouse Lumbar,Mouse Lung,Mouse Lymph,Mouse Lymph node,Mouse Lymphoid tissue,Mouse Macrovessel,Mouse Mammary Gland,Mouse Mammary gland,Mouse Meniscus,Mouse Muscle,Mouse Nerve,Mouse Neural tube,Mouse Nodose,Mouse Non-Vasculature,Mouse Nose,Mouse Omentum,Mouse Oral cavity,Mouse Ovary,Mouse Pancreas,Mouse PeriBiliary cell gland,Mouse Peribiliary gland,Mouse Peritoneal cavity,Mouse Peritoneum,Mouse Peyer patch,Mouse Pharynx,Mouse Prostate,Mouse Pylorus,Mouse Renal Tubule,Mouse Salivary gland,Mouse Scalp,Mouse Skeletal muscle,Mouse Skin,Mouse Soft tissue,Mouse Spinal column,Mouse Spinal cord,Mouse Spleen,Mouse Stomach,Mouse Suprarenal gland,Mouse Sural nerve,Mouse Tendon,Mouse Testis,Mouse Thymus,Mouse Thyroid,Mouse Tongue,Mouse Tonsil,Mouse Tooth,Mouse Trachea,Mouse Umbilical cord,Mouse Undefined,Mouse Uterine cervix,Mouse Uterus,Mouse Vagina,Mouse Vein,Mouse limb,Mouse lymph node'
param[['enrichrDatabase']] = 'Tabula_Muris,Tabula_Sapiens,Azimuth_Cell_Types_2021,PanglaoDB_Augmented_2021,CellMarker_Augmented_2021,Allen_Brain_Atlas_10x_scRNA_2021,Human_Gene_Atlas,Mouse_Gene_Atlas'
param[['Azimuth']] = 'none'
param[['SingleR']] = 'none'
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']] = 'p6007/o5495_o5444_ScSeurat_2024-12-05--09-59-39'
param[['isLastJob']] = FALSE
output = list()
output[['Name']] = 'Undifferentiated_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]']] = 'p6007/o5495_o5444_ScSeurat_2024-12-05--09-59-39/Undifferentiated_lung_cells_SCReport/00index.html'
output[['SC Cluster Report [File]']] = 'p6007/o5495_o5444_ScSeurat_2024-12-05--09-59-39/Undifferentiated_lung_cells_SCReport'
output[['SC Seurat']] = 'p6007/o5495_o5444_ScSeurat_2024-12-05--09-59-39/Undifferentiated_lung_cells_SCReport/scData.qs'
output[['Condition [Factor]']] = 'Undifferentiated'
output[['Sample Id [B-Fabric]']] = 'bfs_194151'
output[['Order Id [B-Fabric]']] = '5495'
input = list()
input[['Name']] = 'Undifferentiated_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/Undifferentiated_lung_cells'
input[['Report']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Undifferentiated_lung_cells/web_summary.html'
input[['CountMatrix']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Undifferentiated_lung_cells/filtered_feature_bc_matrix'
input[['UnfilteredCountMatrix']] = 'p6000/o5495_o5444_CellRangerCount_2024-03-18--11-52-08/Undifferentiated_lung_cells/raw_feature_bc_matrix'
input[['Read Count']] = '342606804'
input[['Condition']] = 'Undifferentiated'
input[['Sample Id']] = 'bfs_194151'
input[['Order Id']] = '5495'
EzAppScSeurat\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r Undifferentiated_lung_cells_SCReport /srv/GT/analysis/course_sushi/public/gstore/projects/p6007/o5495_o5444_ScSeurat_2024-12-05--09-59-39/
cd /scratch
rm -rf /scratch/o5495_o5444_ScSeurat_2024-12-05--09-59-39_Undifferentiated_lung_cells_temp$$ || exit 1


echo __SCRIPT END__