resources:
  directories:
    root: /XXX/XXX/XXX/XXXX/BulkRNA_BALL_Integration
    conda_dir: . # if not required set to "."
    reference: reference
    data: input-fastq
    progs: progs
    results: results
    qual_check: 01-qcheck
    trimming: 02-trim
    alignments: 03-aln
    counts: 04-counts_bypatient
    dge: 05-DGE_bypatient_0.1
    post: 06-post-analysis_bypatient_0.1
    cluster: 07-cluster-analysis_bypatient_0.1
  organism: human # choices: human mouse ...
  genome: GRCh38.primary_assembly.genome.fa # 
  genome_annot: gencode.v34.primary_assembly.gtf # skipped - counts already present
  design: patient,condition # cov1,cov2,...,condition
  seq_type: single-end # choices: single-end paired-end # skipped - counts already present
  strand_type: unstranded # choices: unstranded stranded reverse # skipped - counts already present
  fdr_thr: 0.1
  logfc_thr: 0
  rand_walk: 1 # choices: 0 (do not print random walks) 1 (print random walks)
  post_analysis_tool: DESeq # choices: edgeR DESeq limma
  fastqfiles:
    - PT10_395C0H: C0_HIGH_S13
    - PT10_395C0L: C0_LOW_S14
    - PT10_395C1H: C1_HIGH_S9
    - PT10_395C1L: C1_LOW_S10
    - PT10_395C3H: C3_HIGH_S11
    - PT10_395C3L: C3_LOW_S12
    - PT12_27C3R3L: C3_R3_S1
    - PT12_27C3R4H: C3_R4_S2
    - PT12_27D1R3L: D1_R3_S7
    - PT12_27D1R4H: D1_R4_S8
    - PT12_27D2R3L: D2_R3_S9
    - PT12_27D2R4H: D2_R4_S10
    - PT13_37C0R4H: 1_S1_L001,1_S1_L002
    - PT13_37C0R5L: 2_S2_L001,2_S2_L002
    - PT13_37C1R4H: 3_S3_L001,3_S3_L002
    - PT13_37C1R5L: 4_S4_L001,4_S4_L002
#NON USARE TRATTINI
  samples:
    - PT10_395C0H: PT10_395,GFP_HIGH
    - PT10_395C0L: PT10_395,GFP_LOW
    - PT10_395C1H: PT10_395,GFP_HIGH
    - PT10_395C1L: PT10_395,GFP_LOW
    - PT10_395C3H: PT10_395,GFP_HIGH
    - PT10_395C3L: PT10_395,GFP_LOW
    - PT12_27C3R3L: PT12_27,GFP_LOW
    - PT12_27C3R4H: PT12_27,GFP_HIGH
    - PT12_27D1R3L: PT12_27,GFP_LOW
    - PT12_27D1R4H: PT12_27,GFP_HIGH
    - PT12_27D2R3L: PT12_27,GFP_LOW
    - PT12_27D2R4H: PT12_27,GFP_HIGH
    - PT13_37C0R4H: PT13_37,GFP_HIGH
    - PT13_37C0R5L: PT13_37,GFP_LOW
    - PT13_37C1R4H: PT13_37,GFP_HIGH
    - PT13_37C1R5L: PT13_37,GFP_LOW
  contrasts:
    - GFP_LOW:GFP_HIGH
  enrichergmtfiles:
    - c1.all.v7.0.symbols.gmt
    - c2.all.v7.0.symbols.gmt
    - c3.all.v7.0.symbols.gmt
    - c4.all.v7.0.symbols.gmt
    - c5.all.v7.0.symbols.gmt
    - c6.all.v7.0.symbols.gmt
    - c7.all.v7.0.symbols.gmt
    - h.all.v7.0.symbols.gmt
  read1_mask: "_R1_001.fastq.gz"
  read2_mask: "_R2_001.fastq.gz"
  read_mask: "_R1_001.fastq.gz"