Added RNAseq config file.

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"