#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-02-26--16-15-22/scripts/Transcriptomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh
set -eux
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-02-26--16-15-22/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']] = 'rnaseq'
param[['pipelineVersion']] = '3.19.0'
param[['inputType']] = 'samplesheet'
param[['samplesheetMapping']] = '{"sample":"Name","fastq_1":"Read1 [File]","fastq_2":"Read2 [File]","strandedness":"StrandMode"}'
param[['pseudo_aligner']] = ''
param[['skip_alignment']] = ''
param[['multiqc_title']] = ''
param[['genome']] = ''
param[['fasta']] = ''
param[['gtf']] = ''
param[['gff']] = ''
param[['gene_bed']] = ''
param[['transcript_fasta']] = ''
param[['additional_fasta']] = ''
param[['splicesites']] = ''
param[['star_index']] = ''
param[['hisat2_index']] = ''
param[['rsem_index']] = ''
param[['salmon_index']] = ''
param[['kallisto_index']] = ''
param[['hisat2_build_memory']] = '200.GB'
param[['gencode']] = 'false'
param[['gtf_extra_attributes']] = 'gene_name'
param[['gtf_group_features']] = 'gene_id'
param[['featurecounts_group_type']] = 'gene_biotype'
param[['featurecounts_feature_type']] = 'exon'
param[['trimmer']] = 'trimgalore'
param[['extra_trimgalore_args']] = ''
param[['extra_fastp_args']] = ''
param[['min_trimmed_reads']] = '10000'
param[['bbsplit_fasta_list']] = ''
param[['bbsplit_index']] = ''
param[['sortmerna_index']] = ''
param[['remove_ribo_rna']] = 'false'
param[['ribo_database_manifest']] = '${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt'
param[['with_umi']] = 'false'
param[['umi_dedup_tool']] = 'umitools'
param[['umitools_extract_method']] = 'string'
param[['umitools_bc_pattern']] = ''
param[['umitools_bc_pattern2']] = ''
param[['umi_discard_read']] = '0'
param[['umitools_umi_separator']] = ''
param[['umitools_grouping_method']] = 'unique'
param[['umitools_dedup_stats']] = 'false'
param[['aligner']] = 'star_salmon'
param[['pseudo_aligner_kmer_size']] = '31'
param[['bam_csi_index']] = 'false'
param[['star_ignore_sjdbgtf']] = 'false'
param[['salmon_quant_libtype']] = 'A'
param[['min_mapped_reads']] = '5'
param[['seq_center']] = ''
param[['stringtie_ignore_gtf']] = 'false'
param[['extra_star_align_args']] = ''
param[['extra_salmon_quant_args']] = ''
param[['extra_kallisto_quant_args']] = ''
param[['kallisto_quant_fraglen']] = '200'
param[['kallisto_quant_fraglen_sd']] = '200'
param[['stranded_threshold']] = '0.8'
param[['unstranded_threshold']] = '0.1'
param[['save_merged_fastq']] = 'false'
param[['save_umi_intermeds']] = 'false'
param[['save_non_ribo_reads']] = 'false'
param[['save_bbsplit_reads']] = 'false'
param[['save_reference']] = 'false'
param[['save_trimmed']] = 'false'
param[['save_align_intermeds']] = 'false'
param[['save_unaligned']] = 'false'
param[['save_kraken_assignments']] = 'false'
param[['save_kraken_unassigned']] = 'false'
param[['extra_fqlint_args']] = '--disable-validator P001'
param[['deseq2_vst']] = 'true'
param[['rseqc_modules']] = 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'
param[['contaminant_screening']] = 'kraken2'
param[['kraken_db']] = ''
param[['bracken_precision']] = 'D'
param[['skip_gtf_filter']] = 'false'
param[['skip_gtf_transcript_filter']] = 'false'
param[['skip_bbsplit']] = 'true'
param[['skip_umi_extract']] = 'false'
param[['skip_linting']] = 'false'
param[['skip_trimming']] = 'false'
param[['skip_pseudo_alignment']] = 'false'
param[['skip_markduplicates']] = 'false'
param[['skip_bigwig']] = 'false'
param[['skip_stringtie']] = 'false'
param[['skip_fastqc']] = 'false'
param[['skip_preseq']] = 'true'
param[['skip_dupradar']] = 'false'
param[['skip_qualimap']] = 'false'
param[['skip_rseqc']] = 'false'
param[['skip_biotype_qc']] = 'false'
param[['skip_deseq2_qc']] = 'false'
param[['skip_multiqc']] = 'false'
param[['skip_qc']] = 'false'
param[['sushi_app']] = 'NfCoreRnaseqApp'
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/NfCoreRnaseq_2026-02-26--16-15-22'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = ''
output[['Result [File]']] = 'p1001/NfCoreRnaseq_2026-02-26--16-15-22/_result'
output[['MultiQC [Link]']] = 'p1001/NfCoreRnaseq_2026-02-26--16-15-22/_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/NfCoreRnaseq_2026-02-26--16-15-22/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/NfCoreRnaseq_2026-02-26--16-15-22/
cd /scratch
rm -rf /scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp$$ || exit 1