config.yaml

---
blast:
  evalue: 1e-10
  maxTargets: "1"
  outFmt: "6 qseqid evalue length mismatch salltitles"
deseq2:
  maxfraction: "0.7"
fastp:
  qualified_quality_phred: 15
filter_for_plots:
  average_samples: "yes"
  maximum_pvalue: "0.05"
  minimum_foldchange: "2"
  minimum_reads: "100"
make_plots:
  colour_of_heatmap: "c(\"white\",\"green\",\"green4\",\"violet\",\"purple\")"
  height_in_dendrogram: "1.5"
  membership_min: "0.2"
  method_of_clustering: pam
  number_of_clusters: "2"
  opt_clust_number: average_silhouette_width
refs:
  annotation: annotations/Petunia_axillaris_v1.6.2_proteins.mapman_annotation.txt.gz
  genome: "ftp://ftp.solgenomics.net/genomes/Petunia_axillaris/assembly/Petunia_axillaris_v1.6.2_genome.fasta"
  proteins_fasta: "ftp://ftp.solgenomics.net/genomes/Petunia_axillaris/annotation/Petunia_axillaris_v1.6.2_proteins.fasta"
  transcriptome_gtf: "ftp://ftp.solgenomics.net/genomes/Petunia_axillaris/annotation/Petunia_axillaris_v1.6.2_gene_models.gff"
result_dir: results/
trimmomatic:
  LeadMinTrimQual: "3"
  TrailMinTrimQual: "3"
  adapters: adapters.fasta
  avgMinQual: "15"
  minReadLength: "40"
  palindromeClipTreshold: "30"
  phred: "-phred33"
  seedMisMatches: "2"
  simpleClipThreshold: "10"
  windowSize: "4"
units: samples.tsv
working_dir: temp/