config.yaml

resources:
  directories:
    root: vavassori_lnp2022_rnaseq_lnps
    conda_dir: anaconda3/envs/rnaseq # if not required set to "."
    reference: reference
    data: input-fastq
    progs: rna-seq
    results: results
    qual_check: 01-qcheck
    trimming: 02-trim
    alignments: 03-aln
    counts: 04-counts-T # HSPC
    dge: 05-DGE-T # HSPC
    post: 06-post-analysis-T # HSPC
  organism: human # choices: human mouse ...
  genome: GRCh38.v35
  genome_annot: gencode.v35.primary_assembly.annotation.gtf
  design: donor,condition # cov1,cov2,...,condition
  seq_type: paired-end # choices: single-end paired-end
  strand_type: unstranded # choices: unstranded stranded reverse
  fdr_thr: 0.05
  logfc_thr: 0
  rand_walk: 0 # choices: 0 (do not print random walks) 1 (print random walks)
  post_analysis_tool: DESeq # choices: edgeR DESeq
  fastqfiles:
    #- Sample1: S1
    #- Sample2: S2
    #- Sample3: S3
    #- Sample4: S4
    #- Sample5: S5
    #- Sample6: S6
    #- Sample7: S7
    #- Sample8: S8
    #- Sample9: S9
    #- Sample10: S10
    #- Sample11: S11
    #- Sample12: S12
    #- Sample13: S13
    #- Sample14: S14
    #- Sample15: S15
    #- Sample16: S16
    #- Sample17: S17
    #- Sample18: S18
    - Sample19: S19
    - Sample20: S20
    - Sample21: S21
    - Sample22: S22
    - Sample23: S23
    - Sample24: S24
    - Sample25: S25
    - Sample26: S26
    - Sample27: S27
    - Sample28: S28
    - Sample29: S29
    - Sample30: S30
    - Sample31: S31
    - Sample32: S32
    - Sample33: S33
    - Sample34: S34
    - Sample35: S35
    - Sample36: S36
  samples:
    #- Sample1: HSPC_UT
    #- Sample2: HSPC_UTelectro
    #- Sample3: HSPC_electroRNP
    #- Sample4: HSPC_electroRNA
    #- Sample5: HSPC_emptyLNPs
    #- Sample6: HSPC_LNPsRNA
    #- Sample7: HSPC_UT
    #- Sample8: HSPC_UTelectro
    #- Sample9: HSPC_electroRNP
    #- Sample10: HSPC_electroRNA
    #- Sample11: HSPC_emptyLNPs
    #- Sample12: HSPC_LNPsRNA
    #- Sample13: HSPC_UT
    #- Sample14: HSPC_UTelectro
    #- Sample15: HSPC_electroRNP
    #- Sample16: HSPC_electroRNA
    #- Sample17: HSPC_emptyLNPs
    #- Sample18: HSPC_LNPsRNA
    - Sample19: Donor1,T_UT
    - Sample20: Donor1,T_UTelectro
    - Sample21: Donor1,T_electroRNP
    - Sample22: Donor1,T_electroRNA
    - Sample23: Donor1,T_emptyLNPs
    - Sample24: Donor1,T_LNPsRNA
    - Sample25: Donor2,T_UT
    - Sample26: Donor2,T_UTelectro
    - Sample27: Donor2,T_electroRNP
    - Sample28: Donor2,T_electroRNA
    - Sample29: Donor2,T_emptyLNPs
    - Sample30: Donor2,T_LNPsRNA
    - Sample31: Donor3,T_UT
    - Sample32: Donor3,T_UTelectro
    - Sample33: Donor3,T_electroRNP
    - Sample34: Donor3,T_electroRNA
    - Sample35: Donor3,T_emptyLNPs
    - Sample36: Donor3,T_LNPsRNA
  contrasts:
    # - HSPC_UTelectro:HSPC_UT
    # - HSPC_electroRNP:HSPC_UT
    # - HSPC_electroRNA:HSPC_UT
    # - HSPC_emptyLNPs:HSPC_UT
    # - HSPC_LNPsRNA:HSPC_UT
    # - HSPC_electroRNP:HSPC_UTelectro
    # - HSPC_electroRNA:HSPC_UTelectro
    # - HSPC_emptyLNPs:HSPC_UTelectro
    # - HSPC_LNPsRNA:HSPC_UTelectro
    # - HSPC_electroRNA:HSPC_electroRNP
    # - HSPC_emptyLNPs:HSPC_electroRNP
    # - HSPC_LNPsRNA:HSPC_electroRNP
    # - HSPC_emptyLNPs:HSPC_electroRNA
    # - HSPC_LNPsRNA:HSPC_electroRNA
    # - HSPC_LNPsRNA:HSPC_emptyLNPs
    - T_UTelectro:T_UT
    - T_electroRNP:T_UT
    - T_electroRNA:T_UT
    - T_emptyLNPs:T_UT
    - T_LNPsRNA:T_UT
    - T_electroRNP:T_UTelectro
    - T_electroRNA:T_UTelectro
    - T_emptyLNPs:T_UTelectro
    - T_LNPsRNA:T_UTelectro
    - T_electroRNA:T_electroRNP
    - T_emptyLNPs:T_electroRNP
    - T_LNPsRNA:T_electroRNP
    - T_emptyLNPs:T_electroRNA
    - T_LNPsRNA:T_electroRNA
    - T_LNPsRNA:T_emptyLNPs
  enrichergmtfiles:
    - h.all.v7.2.symbols.gmt
  read1_mask: "_R1_001.fastq.gz"
  read2_mask: "_R2_001.fastq.gz"
  read_mask: "_R1_001.fastq.gz"