#!/bin/bash
#/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreEager_2026-03-24--15-47-18/scripts/Metagenomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh
set -eux
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/NfCoreEager_2026-03-24--15-47-18_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreEager_2026-03-24--15-47-18/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']] = '16'
param[['ram']] = '128'
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']] = 'eager'
param[['pipelineVersion']] = '2.5.3'
param[['inputType']] = 'unknown'
param[['nextflowModuleVersion']] = '25.10'
param[['udg_type']] = 'none'
param[['single_stranded']] = 'false'
param[['single_end']] = 'false'
param[['colour_chemistry']] = '4'
param[['bam']] = 'false'
param[['snpcapture_bed']] = ''
param[['run_convertinputbam']] = 'false'
param[['fasta']] = ''
param[['genome']] = ''
param[['bwa_index']] = ''
param[['bt2_index']] = ''
param[['fasta_index']] = ''
param[['seq_dict']] = ''
param[['large_ref']] = 'false'
param[['save_reference']] = 'false'
param[['skip_fastqc']] = 'false'
param[['skip_adapterremoval']] = 'false'
param[['skip_preseq']] = 'false'
param[['skip_deduplication']] = 'false'
param[['skip_damage_calculation']] = 'false'
param[['skip_qualimap']] = 'false'
param[['complexity_filter_poly_g']] = 'false'
param[['complexity_filter_poly_g_min']] = '10'
param[['clip_forward_adaptor']] = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
param[['clip_reverse_adaptor']] = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
param[['clip_adapters_list']] = ''
param[['clip_readlength']] = '30'
param[['clip_min_read_quality']] = '20'
param[['min_adap_overlap']] = '1'
param[['skip_collapse']] = 'false'
param[['skip_trim']] = 'false'
param[['preserve5p']] = 'false'
param[['mergedonly']] = 'false'
param[['qualitymax']] = '41'
param[['run_post_ar_trimming']] = 'false'
param[['post_ar_trim_front']] = '7'
param[['post_ar_trim_tail']] = '7'
param[['post_ar_trim_front2']] = '7'
param[['post_ar_trim_tail2']] = '7'
param[['mapper']] = 'bwaaln'
param[['bwaalnn']] = '0.01'
param[['bwaalnk']] = '2'
param[['bwaalnl']] = '1024'
param[['bwaalno']] = '2'
param[['circularextension']] = '500'
param[['circulartarget']] = 'MT'
param[['circularfilter']] = 'false'
param[['bt2_alignmode']] = 'local'
param[['bt2_sensitivity']] = 'no-preset'
param[['bt2n']] = '0'
param[['bt2l']] = '0'
param[['bt2_trim5']] = '0'
param[['bt2_trim3']] = '0'
param[['bt2_maxins']] = '500'
param[['hostremoval_input_fastq']] = 'false'
param[['hostremoval_mode']] = 'strip'
param[['run_bam_filtering']] = 'false'
param[['bam_mapping_quality_threshold']] = '0'
param[['bam_filter_minreadlength']] = '0'
param[['bam_unmapped_type']] = 'discard'
param[['dedupper']] = 'markduplicates'
param[['dedup_all_merged']] = 'false'
param[['preseq_mode']] = 'c_curve'
param[['preseq_step_size']] = '1000'
param[['preseq_maxextrap']] = '10000000000'
param[['preseq_terms']] = '100'
param[['preseq_bootstrap']] = '100'
param[['preseq_cval']] = '0.95'
param[['damage_calculation_tool']] = 'damageprofiler'
param[['damageprofiler_length']] = '100'
param[['damageprofiler_threshold']] = '15'
param[['damageprofiler_yaxis']] = '0.3'
param[['mapdamage_downsample']] = '0'
param[['mapdamage_yaxis']] = '0.3'
param[['run_pmdtools']] = 'false'
param[['pmdtools_range']] = '10'
param[['pmdtools_threshold']] = '3'
param[['pmdtools_reference_mask']] = ''
param[['pmdtools_max_reads']] = '10000'
param[['pmdtools_platypus']] = 'false'
param[['run_mapdamage_rescaling']] = 'false'
param[['rescale_seqlength']] = '12'
param[['rescale_length_5p']] = '0'
param[['rescale_length_3p']] = '0'
param[['run_bedtools_coverage']] = 'false'
param[['anno_file']] = ''
param[['anno_file_is_unsorted']] = 'false'
param[['run_trim_bam']] = 'false'
param[['bamutils_clip_double_stranded_half_udg_left']] = '0'
param[['bamutils_clip_double_stranded_half_udg_right']] = '0'
param[['bamutils_clip_double_stranded_none_udg_left']] = '0'
param[['bamutils_clip_double_stranded_none_udg_right']] = '0'
param[['bamutils_clip_single_stranded_half_udg_left']] = '0'
param[['bamutils_clip_single_stranded_half_udg_right']] = '0'
param[['bamutils_clip_single_stranded_none_udg_left']] = '0'
param[['bamutils_clip_single_stranded_none_udg_right']] = '0'
param[['bamutils_softclip']] = 'false'
param[['run_genotyping']] = 'false'
param[['genotyping_tool']] = 'ug'
param[['genotyping_source']] = 'raw'
param[['gatk_call_conf']] = '30'
param[['gatk_ploidy']] = '2'
param[['gatk_downsample']] = '250'
param[['gatk_dbsnp']] = ''
param[['gatk_hc_out_mode']] = 'EMIT_ALL_ACTIVE_SITES'
param[['gatk_hc_emitrefconf']] = 'NONE'
param[['gatk_ug_out_mode']] = 'EMIT_ALL_SITES'
param[['gatk_ug_genotype_model']] = 'SNP'
param[['gatk_ug_keep_realign_bam']] = 'false'
param[['gatk_ug_defaultbasequalities']] = ''
param[['freebayes_C']] = '1'
param[['freebayes_g']] = '0'
param[['freebayes_p']] = '2'
param[['pileupcaller_bedfile']] = ''
param[['pileupcaller_snpfile']] = ''
param[['pileupcaller_method']] = 'randomHaploid'
param[['pileupcaller_transitions_mode']] = 'AllSites'
param[['pileupcaller_min_map_quality']] = '30'
param[['pileupcaller_min_base_quality']] = '30'
param[['angsd_glmodel']] = 'samtools'
param[['angsd_glformat']] = 'text'
param[['angsd_createfasta']] = 'false'
param[['angsd_fastamethod']] = 'random'
param[['run_bcftools_stats']] = 'true'
param[['run_vcf2genome']] = 'false'
param[['vcf2genome_outfile']] = ''
param[['vcf2genome_header']] = ''
param[['vcf2genome_minc']] = '5'
param[['vcf2genome_minq']] = '30'
param[['vcf2genome_minfreq']] = '0.8'
param[['run_multivcfanalyzer']] = 'false'
param[['write_allele_frequencies']] = 'false'
param[['min_genotype_quality']] = '30'
param[['min_base_coverage']] = '5'
param[['min_allele_freq_hom']] = '0.9'
param[['min_allele_freq_het']] = '0.9'
param[['additional_vcf_files']] = ''
param[['reference_gff_annotations']] = 'NA'
param[['reference_gff_exclude']] = 'NA'
param[['snp_eff_results']] = 'NA'
param[['run_mtnucratio']] = 'false'
param[['mtnucratio_header']] = 'MT'
param[['run_sexdeterrmine']] = 'false'
param[['sexdeterrmine_bedfile']] = ''
param[['run_nuclear_contamination']] = 'false'
param[['contamination_chrom_name']] = 'X'
param[['metagenomic_complexity_filter']] = 'false'
param[['metagenomic_complexity_entropy']] = '0.3'
param[['run_metagenomic_screening']] = 'false'
param[['metagenomic_tool']] = ''
param[['database']] = ''
param[['metagenomic_min_support_reads']] = '1'
param[['percent_identity']] = '85'
param[['malt_mode']] = 'BlastN'
param[['malt_alignment_mode']] = 'Local'
param[['malt_top_percent']] = '1'
param[['malt_min_support_mode']] = 'percent'
param[['malt_min_support_percent']] = '0.01'
param[['malt_max_queries']] = '100'
param[['malt_memory_mode']] = 'load'
param[['malt_sam_output']] = 'false'
param[['run_maltextract']] = 'false'
param[['maltextract_taxon_list']] = ''
param[['maltextract_ncbifiles']] = ''
param[['maltextract_filter']] = 'def_anc'
param[['maltextract_toppercent']] = '0.01'
param[['maltextract_destackingoff']] = 'false'
param[['maltextract_downsamplingoff']] = 'false'
param[['maltextract_duplicateremovaloff']] = 'false'
param[['maltextract_matches']] = 'false'
param[['maltextract_megansummary']] = 'false'
param[['maltextract_percentidentity']] = '85'
param[['maltextract_topalignment']] = 'false'
param[['sushi_app']] = 'NfCoreEagerApp'
param[['refBuild']] = 'Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p1001/NfCoreEager_2026-03-24--15-47-18'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = ''
output[['Result [File]']] = 'p1001/NfCoreEager_2026-03-24--15-47-18/_result'
output[['MultiQC [Link]']] = 'p1001/NfCoreEager_2026-03-24--15-47-18/_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/NfCoreEager_2026-03-24--15-47-18/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/NfCoreEager_2026-03-24--15-47-18/
cd /scratch
rm -rf /scratch/NfCoreEager_2026-03-24--15-47-18_temp$$ || exit 1