config.yaml

# reference
genome:
  fasta: /data/wenyuhao/55/gencodegenes/GRCh38.p13.genome.fa
  star_index: /data/wenyuhao/55/gencodegenes/index
  gtf: /data/wenyuhao/55/gencodegenes/gencode.v41.annotation.gtf
  geneset:
    go: /data/wenyuhao/GSEA/c5.go.v2022.1.Hs.symbols.gmt
    kegg: /data/wenyuhao/GSEA/c2.cp.kegg.v2022.1.Hs.symbols.gmt

# output plots formats
plot_formats:
  - pdf
  - png

# workspace for all jobs to run the pipeline
# all of your output will be place in this dir
workspace: /data/wenyuhao/tmp/RNAseq/out1

samples:
  293F_rep1:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129609_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129609_2.fastq.gz
    meta:
      cell: 293F
      rep: rep1
      group: 293F
  293F_rep2:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129629_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129629_1.fastq.gz
    meta:
      cell: 293F
      rep: rep2
      group: 293F
  293F_rep3:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129630_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129630_2.fastq.gz
    meta:
      cell: 293F
      rep: rep3
      group: 293F

  293E_rep1:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129610_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129610_2.fastq.gz
    meta:
      cell: 293E
      rep: rep1
      group: 293E
  293E_rep2:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129611_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129611_1.fastq.gz
    meta:
      cell: 293E
      rep: rep2
      group: 293E
  293E_rep3:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129612_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129612_2.fastq.gz
    meta:
      cell: 293E
      rep: rep3
      group: 293E

  293T_rep1:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129623_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129623_2.fastq.gz
    meta:
      cell: 293T
      rep: rep1
      group: 293T
  293T_rep2:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129624_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129624_1.fastq.gz
    meta:
      cell: 293T
      rep: rep2
      group: 293T
  293T_rep3:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129625_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129625_2.fastq.gz
    meta:
      cell: 293T
      rep: rep3
      group: 293T

  293H_rep1:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129626_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129626_2.fastq.gz
    meta:
      cell: 293H
      rep: rep1
      group: 293H
  293H_rep2:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129627_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129627_1.fastq.gz
    meta:
      cell: 293H
      rep: rep2
      group: 293H
  293H_rep3:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129628_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129628_2.fastq.gz
    meta:
      cell: 293H
      rep: rep3
      group: 293H

  HEK293_rep1:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129615_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129615_2.fastq.gz
    meta:
      cell: HEK293
      rep: rep1
      group: HEK293
  HEK293_rep2:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129616_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129616_1.fastq.gz
    meta:
      cell: HEK293
      rep: rep2
      group: HEK293
  HEK293_rep3:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129617_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129617_2.fastq.gz
    meta:
      cell: HEK293
      rep: rep3
      group: HEK293

  Freestyle293F_rep1:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129618_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129618_2.fastq.gz
    meta:
      cell: Freestyle293F
      rep: rep1
      group: Freestyle293F
  Freestyle293F_rep2:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129621_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129621_1.fastq.gz
    meta:
      cell: Freestyle293F
      rep: rep2
      group: Freestyle293F
  Freestyle293F_rep3:
    fastq:
      lib1:
        fq1: /data/wenyuhao/tmp/fasgz/SRR10129622_1.fastq.gz
        fq2: /data/wenyuhao/tmp/fasgz/SRR10129622_2.fastq.gz
    meta:
      cell: Freestyle293F
      rep: rep3
      group: Freestyle293F
# comparisons
comparisons:
  HEK293_vs_Freestyle293F:
    condition: group
    numerator: HEK293
    denominator: Freestyle293F
  293F_vs_Freestyle293F:
    condition: group
    numerator: 293F
    denominator: Freestyle293F
  293F_vs_293E:
    condition: group
    numerator: 293F
    denominator: 293E
  293F_vs_293T:
    condition: group
    numerator: 293F
    denominator: 293T
  293F_vs_293H:
    condition: group
    numerator: 293F
    denominator: 293H
  293E_vs_293T:
    condition: group
    numerator: 293E
    denominator: 293T
  293E_vs_293H:
    condition: group
    numerator: 293E
    denominator: 293H
  293T_vs_293H:
    condition: group
    numerator: 293T
    denominator: 293H
  HEK293_vs_293F:
    condition: group
    numerator: HEK293
    denominator: 293F
  HEK293_vs_293E:
    condition: group
    numerator: HEK293
    denominator: 293E
  HEK293_vs_293T:
    condition: group
    numerator: HEK293
    denominator: 293T
  HEK293_vs_293H:
    condition: group
    numerator: HEK293
    denominator: 293H