//Run parameters Thu Sep 04 07:43:21 CEST 2025
params {
aln_filter_mode='paired_rmdup'
containers_base='https://lipm-browsers.toulouse.inra.fr/pub/singularity-repository/mutdetect2'
design='design.csv'
help=false
max_cpus=12
max_line_mutant_position=10000
max_memory=128 GB
max_time=4d
min_line_mutant_position=1
min_line_wt_position=3
mode='run'
monochrome_logs=false
mpileup_parameters=' -B --max-depth 100 '
mpileuprecall_parameters='-B'
outdir='minread_5-minread2_3'
refannot='HanXRQr2.0-SUNRISE-2.1.gff3'
refseq='HanXRQr2.0-SUNRISE-2.1.genome.fasta'
samtools_max_memory='8G'
singularity_pull_docker_container=false
skip_trimmo=true
snpeff_exclude_ann='LOW\|intergenic_variant\|upstream_gene_variant\|intergenic_region'
snpeff_up_downstream_len=1000
trimmo_leading_qual_min=20
trimmo_min_length=50
trimmo_params=' -validatePairs -phred33 '
trimmo_sliding_window_qual=20
trimmo_sliding_window_size=4
trimmo_trailing_qual_min=20
varscan_mutant_avg_qual=20
varscan_mutant_min_coverage=5
varscan_mutant_min_reads2=3
varscan_mutant_pvalue=0.01
varscan_mutant_var_freq=0.2
varscan_mutant_var_freq_for_hom=0.8
varscan_wt_avg_qual=15
varscan_wt_min_coverage=5
varscan_wt_min_reads2=4
varscan_wt_pvalue=0.01
varscan_wt_var_freq=0.2
varscan_wt_var_freq_for_hom=0.8
verbose=false
version=[pipeline:1.0, trimmomatic:0.39, bwa:0.7.17, snpeff:5.1, tabix:1.9, lipmutils:1.0, samtools:1.9, bcftools:1.9, varscan:2.4.4, vcftools:0.1.16]
wt_genotype='WT'
}