#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/scripts/Epigenetics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh
set -eux
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/NfCoreChipseq_2026-02-26--13-55-19_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/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


#### NOW THE ACTUAL JOBS STARTS
export NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/
export SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/
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)
}
source('/srv/GT/analysis/masaomi/2026/FGCZ/nf_core_sushi_app_20260109/EzAppNfCoreGeneric.R')
param = list()
param[['cores']] = '8'
param[['ram']] = '30'
param[['scratch']] = '100'
param[['partition']] = 'user'
param[['process_mode']] = 'DATASET'
param[['samples']] = 'S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff'
param[['nfcorePipeline']] = 'chipseq'
param[['pipelineVersion']] = '2.1.0'
param[['inputType']] = 'samplesheet'
param[['samplesheetMapping']] = '{"sample":"Name","fastq_1":"Read1 [File]","fastq_2":"Read2 [File]","replicate":"Replicate","antibody":"Antibody","control":"Control"}'
param[['fasta']] = '/srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa'
param[['fragment_size']] = '200'
param[['seq_center']] = ''
param[['read_length']] = '50'
param[['multiqc_title']] = ''
param[['genome']] = ''
param[['gtf']] = ''
param[['gff']] = ''
param[['bwa_index']] = ''
param[['bowtie2_index']] = ''
param[['chromap_index']] = ''
param[['star_index']] = ''
param[['gene_bed']] = ''
param[['macs_gsize']] = ''
param[['blacklist']] = ''
param[['save_reference']] = 'false'
param[['clip_r1']] = '2'
param[['clip_r2']] = '2'
param[['three_prime_clip_r1']] = '0'
param[['three_prime_clip_r2']] = '0'
param[['trim_nextseq']] = '0'
param[['skip_trimming']] = 'false'
param[['save_trimmed']] = 'false'
param[['aligner']] = 'bwa'
param[['keep_dups']] = 'false'
param[['keep_multi_map']] = 'false'
param[['bwa_min_score']] = '0'
param[['save_align_intermeds']] = 'false'
param[['save_unaligned']] = 'false'
param[['narrow_peak']] = 'false'
param[['broad_cutoff']] = '0.1'
param[['macs_fdr']] = ''
param[['macs_pvalue']] = ''
param[['min_reps_consensus']] = '1'
param[['save_macs_pileup']] = 'false'
param[['skip_peak_qc']] = 'false'
param[['skip_peak_annotation']] = 'false'
param[['skip_consensus_peaks']] = 'false'
param[['skip_fastqc']] = 'false'
param[['skip_picard_metrics']] = 'false'
param[['skip_preseq']] = 'false'
param[['deseq2_vst']] = 'true'
param[['skip_plot_profile']] = 'false'
param[['skip_plot_fingerprint']] = 'false'
param[['skip_spp']] = 'false'
param[['skip_deseq2_qc']] = 'false'
param[['skip_igv']] = 'false'
param[['skip_multiqc']] = 'false'
param[['skip_qc']] = 'false'
param[['sushi_app']] = 'NfCoreChipseqApp'
param[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/NfCoreChipseq_2026-02-26--13-55-19'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = ''
output[['Result [File]']] = 'p1001/NfCoreChipseq_2026-02-26--13-55-19/_result'
output[['MultiQC [Link]']] = 'p1001/NfCoreChipseq_2026-02-26--13-55-19/_result/multiqc/multiqc_report.html'
output[['Tube [Characteristic]']] = 'p3009_5638/7'
output[['Condition [Factor]']] = 'undiff'
output[['Adapter1']] = 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
output[['strandMode']] = 'antisense'
output[['LibraryPrepKit']] = 'Lexogen_mRNA_stranded'
output[['EnrichmentMethod']] = 'PolyA_mRNA_Lexogen_stranded'
output[['InputAmount [Characteristic]']] = '100'
output[['Read Count']] = '100000'
output[['Treatment (Factor)']] = ''
grandchild_output = list()
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/input_dataset.tsv'
EzAppNfCoreGeneric\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r _result /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/
cd /scratch
rm -rf /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp$$ || exit 1