config.yaml

---
wrapper:
  base_url: https://github.com/hermidalc/snakemake-wrappers/raw/main

tmp_dir: /tmp

random_seed: 777

download:
  retries: 5

samples: config/samples.tsv
units: config/units.tsv

studies:
  - A_vs_B
experiments:
  - Experiment1
  - Experiment2

gencode:
  protocol: ftp
  species: mouse
  release: M30
  build: GRCm39
  regions: PRI
  annot:
    fmt: gtf
  gene_annot:
    length_col: Length

fastq:
  data_dir: data/fastq
  pairs:
    - R1_001
    - R2_001
  ext: fastq.gz
  # only used in STAR-generated BAM headers (no analysis is dependent on platform)
  platform: Illumina

trim:
  activate: true
  fastp:
    threads: 8
    extra_params: --trim_poly_x --detect_adapter_for_pe --correction

star:
  index:
    threads: all
  align:
    sort_bam: true
    threads: all
  # regex specific to GTF style
  sj_filter_chr_regex: "^(?!chrM$).+$"  # "chr([1-9][0-9]?|X|Y)"

rseqc:
  infer_exp:
    sample_size: 1e6

diffexp:
  methods:
    - edger
    - deseq2
    - voom
  conditions: [
    [A, B]
  ]
  fc: 1.1
  padj: 0.05
  padj_meth: BH
  qc:
    types:
      - rle
      - pca
      - mds
    legend: topright
    rle_ylim: [
      [-2, 2]
    ]
  heatmap:
    fig_w: 7
    fig_h: 8

gsea:
  padj: 0.1
  msigdb:
    - category: H
      subcategory: null
      collapse: false
    - category: C2
      subcategory: CGP
      collapse: true
    - category: C2
      subcategory: CP:KEGG
      collapse: true
    - category: C2
      subcategory: CP:REACTOME
      collapse: true
    - category: C5
      subcategory: GO:BP
      collapse: true
    - category: C5
      subcategory: GO:CC
      collapse: true
    - category: C5
      subcategory: GO:MF
      collapse: true
    - category: C7
      subcategory: IMMUNESIGDB
      collapse: true
    - category: C8
      subcategory: null
      collapse: false