cores	16
ram	128
scratch	100
partition	user
process_mode	DATASET
samples	S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff
nfcorePipeline	eager
pipelineVersion	2.5.3
inputType	unknown
nextflowModuleVersion	25.10
udg_type	none
single_stranded	false
single_end	false
colour_chemistry	4
bam	false
snpcapture_bed	""
run_convertinputbam	false
fasta	""
genome	""
bwa_index	""
bt2_index	""
fasta_index	""
seq_dict	""
large_ref	false
save_reference	false
skip_fastqc	false
skip_adapterremoval	false
skip_preseq	false
skip_deduplication	false
skip_damage_calculation	false
skip_qualimap	false
complexity_filter_poly_g	false
complexity_filter_poly_g_min	10
clip_forward_adaptor	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
clip_reverse_adaptor	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
clip_adapters_list	""
clip_readlength	30
clip_min_read_quality	20
min_adap_overlap	1
skip_collapse	false
skip_trim	false
preserve5p	false
mergedonly	false
qualitymax	41
run_post_ar_trimming	false
post_ar_trim_front	7
post_ar_trim_tail	7
post_ar_trim_front2	7
post_ar_trim_tail2	7
mapper	bwaaln
bwaalnn	0.01
bwaalnk	2
bwaalnl	1024
bwaalno	2
circularextension	500
circulartarget	MT
circularfilter	false
bt2_alignmode	local
bt2_sensitivity	no-preset
bt2n	0
bt2l	0
bt2_trim5	0
bt2_trim3	0
bt2_maxins	500
hostremoval_input_fastq	false
hostremoval_mode	strip
run_bam_filtering	false
bam_mapping_quality_threshold	0
bam_filter_minreadlength	0
bam_unmapped_type	discard
dedupper	markduplicates
dedup_all_merged	false
preseq_mode	c_curve
preseq_step_size	1000
preseq_maxextrap	10000000000
preseq_terms	100
preseq_bootstrap	100
preseq_cval	0.95
damage_calculation_tool	damageprofiler
damageprofiler_length	100
damageprofiler_threshold	15
damageprofiler_yaxis	0.3
mapdamage_downsample	0
mapdamage_yaxis	0.3
run_pmdtools	false
pmdtools_range	10
pmdtools_threshold	3
pmdtools_reference_mask	""
pmdtools_max_reads	10000
pmdtools_platypus	false
run_mapdamage_rescaling	false
rescale_seqlength	12
rescale_length_5p	0
rescale_length_3p	0
run_bedtools_coverage	false
anno_file	""
anno_file_is_unsorted	false
run_trim_bam	false
bamutils_clip_double_stranded_half_udg_left	0
bamutils_clip_double_stranded_half_udg_right	0
bamutils_clip_double_stranded_none_udg_left	0
bamutils_clip_double_stranded_none_udg_right	0
bamutils_clip_single_stranded_half_udg_left	0
bamutils_clip_single_stranded_half_udg_right	0
bamutils_clip_single_stranded_none_udg_left	0
bamutils_clip_single_stranded_none_udg_right	0
bamutils_softclip	false
run_genotyping	false
genotyping_tool	ug
genotyping_source	raw
gatk_call_conf	30
gatk_ploidy	2
gatk_downsample	250
gatk_dbsnp	""
gatk_hc_out_mode	EMIT_ALL_ACTIVE_SITES
gatk_hc_emitrefconf	NONE
gatk_ug_out_mode	EMIT_ALL_SITES
gatk_ug_genotype_model	SNP
gatk_ug_keep_realign_bam	false
gatk_ug_defaultbasequalities	""
freebayes_C	1
freebayes_g	0
freebayes_p	2
pileupcaller_bedfile	""
pileupcaller_snpfile	""
pileupcaller_method	randomHaploid
pileupcaller_transitions_mode	AllSites
pileupcaller_min_map_quality	30
pileupcaller_min_base_quality	30
angsd_glmodel	samtools
angsd_glformat	text
angsd_createfasta	false
angsd_fastamethod	random
run_bcftools_stats	true
run_vcf2genome	false
vcf2genome_outfile	""
vcf2genome_header	""
vcf2genome_minc	5
vcf2genome_minq	30
vcf2genome_minfreq	0.8
run_multivcfanalyzer	false
write_allele_frequencies	false
min_genotype_quality	30
min_base_coverage	5
min_allele_freq_hom	0.9
min_allele_freq_het	0.9
additional_vcf_files	""
reference_gff_annotations	NA
reference_gff_exclude	NA
snp_eff_results	NA
run_mtnucratio	false
mtnucratio_header	MT
run_sexdeterrmine	false
sexdeterrmine_bedfile	""
run_nuclear_contamination	false
contamination_chrom_name	X
metagenomic_complexity_filter	false
metagenomic_complexity_entropy	0.3
run_metagenomic_screening	false
metagenomic_tool	""
database	""
metagenomic_min_support_reads	1
percent_identity	85
malt_mode	BlastN
malt_alignment_mode	Local
malt_top_percent	1
malt_min_support_mode	percent
malt_min_support_percent	0.01
malt_max_queries	100
malt_memory_mode	load
malt_sam_output	false
run_maltextract	false
maltextract_taxon_list	""
maltextract_ncbifiles	""
maltextract_filter	def_anc
maltextract_toppercent	0.01
maltextract_destackingoff	false
maltextract_downsamplingoff	false
maltextract_duplicateremovaloff	false
maltextract_matches	false
maltextract_megansummary	false
maltextract_percentidentity	85
maltextract_topalignment	false
sushi_app	NfCoreEagerApp
refBuild	Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03