config.yaml

resources:
  directories:
    root: Genewiz_RNAseq_VavassoriV
    conda_dir: anaconda3/envs/rnaseq # 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-D4 # D12
    dge: 05-DGE-D4 # D12
    post: 06-post-analysis-D4 # D12
  organism: human # choices: human mouse ...
  genome: GRCh38.p12
  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: 1--1
    #- Sample2: 2--2
    #- Sample3: 3--3
    - Sample4: 4--4
    - Sample5: 5--5
    - Sample6: 6--6
    - Sample7: 7--7
    - Sample8: 8--8
    - Sample9: 9--9
    - Sample10: 10--10
    - Sample11: 11--11
    - Sample12: 12--12
    - Sample13: 13--13
    - Sample14: 14--14
    - Sample15: 15--15
    - Sample16: 16--16
    - Sample17: 17--17
    - Sample18: 18--18
    #- Sample19: 19--19
    #- Sample20: 20--20
    #- Sample21: 21--21
    #- Sample22: 22--22
    #- Sample23: 23--23
    #- Sample24: 24--24
    #- Sample25: 25--25
    #- Sample26: 26--26
    #- Sample27: 27--27
    #- Sample28: 28--28
    #- Sample29: 29--29
    #- Sample30: 30--30
    #- Sample31: 31--31
    #- Sample32: 32--32
    #- Sample33: 33--33
  samples:
    #- Sample1: Donor1,UT_D3
    #- Sample2: Donor2,UT_D3
    #- Sample3: Donor3,UT_D3
    - Sample4: Donor1,UT_D4
    - Sample5: Donor1,UT_electro_D4
    - Sample6: Donor1,RNP_D4
    - Sample7: Donor1,RNP_AAV6_D4
    - Sample8: Donor1,AAV6_D4
    - Sample9: Donor2,UT_D4
    - Sample10: Donor2,UT_electro_D4
    - Sample11: Donor2,RNP_D4
    - Sample12: Donor2,RNP_AAV6_D4
    - Sample13: Donor2,AAV6_D4
    - Sample14: Donor3,UT_D4
    - Sample15: Donor3,UT_electro_D4
    - Sample16: Donor3,RNP_D4
    - Sample17: Donor3,RNP_AAV6_D4
    - Sample18: Donor3,AAV6_D4
    #- Sample19: Donor1,UT_D12
    #- Sample20: Donor1,UT_electro_D12
    #- Sample21: Donor1,RNP_D12
    #- Sample22: Donor1,RNP_AAV6_D12
    #- Sample23: Donor1,AAV6_D12
    #- Sample24: Donor2,UT_D12
    #- Sample25: Donor2,UT_electro_D12
    #- Sample26: Donor2,RNP_D12
    #- Sample27: Donor2,RNP_AAV6_D12
    #- Sample28: Donor2,AAV6_D12
    #- Sample29: Donor3,UT_D12
    #- Sample30: Donor3,UT_electro_D12
    #- Sample31: Donor3,RNP_D12
    #- Sample32: Donor3,RNP_AAV6_D12
    #- Sample33: Donor3,AAV6_D12
  contrasts:
    - UT_electro_D4:UT_D4
    - RNP_D4:UT_electro_D4
    - RNP_D4:UT_D4
    - AAV6_D4:RNP_D4
    - AAV6_D4:UT_electro_D4
    - AAV6_D4:UT_D4
    - RNP_AAV6_D4:AAV6_D4
    - RNP_AAV6_D4:RNP_D4
    - RNP_AAV6_D4:UT_electro_D4
    - RNP_AAV6_D4:UT_D4
    - UT_electro_D4:AAV6_D4
    - RNP_D4:AAV6_D4
    #- UT_electro_D12:UT_D12
    #- RNP_D12:UT_electro_D12
    #- RNP_D12:UT_D12
    #- AAV6_D12:RNP_D12
    #- AAV6_D12:UT_electro_D12
    #- AAV6_D12:UT_D12
    #- RNP_AAV6_D12:AAV6_D12
    #- RNP_AAV6_D12:RNP_D12
    #- RNP_AAV6_D12:UT_electro_D12
    #- RNP_AAV6_D12:UT_D12
  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"