#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/Canu_2025-11-25--14-43-48/scripts/Assemble_S2_undiff_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh
set -eux
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/Canu_2025-11-25--14-43-48_S2_undiff_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/Canu_2025-11-25--14-43-48/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 Assembly/Canu/2.2 Dev/R/4.5.0 Dev/jdk/21

#### 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']] = '400'
param[['partition']] = 'user'
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff'
param[['canuReadOpt']] = '-pacbio-raw'
param[['canuGenomeSize']] = '5000'
param[['cmdOptions']] = 'useGrid=false'
param[['mail']] = ''
param[['sushi_app']] = 'CanuApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/Canu_2025-11-25--14-43-48'
param[['isLastJob']] = FALSE
output = list()
output[['Name']] = 'S2_undiff'
output[['Reads']] = ''
output[['Draft [File]']] = 'p1001/Canu_2025-11-25--14-43-48/S2_undiff.contigs.fasta'
output[['Condition [Factor]']] = 'undiff'
output[['Tube [Characteristic]']] = 'p3009_5638/2'
output[['InputAmount [Characteristic]']] = '100'
input = list()
input[['Name']] = 'S2_undiff'
input[['Read1']] = 'p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S2_undiff_R1-subsample.fastq.gz'
input[['Species']] = 'Homo sapiens (human)'
input[['Tube']] = 'p3009_5638/2'
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)']] = ''
EzAppCanu\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r S2_undiff.contigs.fasta /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/Canu_2025-11-25--14-43-48/
cd /scratch
rm -rf /scratch/Canu_2025-11-25--14-43-48_S2_undiff_temp$$ || exit 1