| Parameter | Value |
|---|
| 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 |
