Added RNAseq config file.

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"