rnaseq_snakemake/snakefile at main · dimitrisokolowskei/rnaseq_snakemake · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
configfile: "config.yaml"


WORK_DATA = config["WORK_DATA"]
WORK_QC = config["WORK_QC"]
WORK_TRIM = config["WORK_TRIM"]
WORK_KALL = config["WORK_KALL"]


rule all:
    input:
      expand(WORK_QC + "{sample}_{replicate}_fastqc.{extension}", sample=config["samples"], replicate=[1, 2], extension=["zip", "html"]),
      expand(WORK_TRIM + "{sample}_{replicate}_trim.fastq.gz", sample=config["samples"], replicate=[1, 2]),
      WORK_KALL + "Homo_sapiens.GRCh38.cdna.all.index",
      expand(WORK_KALL + "{sample}/abundance.tsv", sample=config["samples"])


rule fastqc:
    input:
      WORK_DATA + "{sample}_{replicate}.fastq.gz"

    output:
      WORK_QC + "{sample}_{replicate}_fastqc.{extension}"

    priority: 50

    threads:
      8

    params:
      path = WORK_QC

    shell:
      "fastqc -t {threads} {input} -o {params.path}"


rule fastp:
    input:
      R1 = WORK_DATA + "{sample}_1.fastq.gz",
      R2 = WORK_DATA + "{sample}_2.fastq.gz"

    output:
       RP = WORK_TRIM + "{sample}_1_trim.fastq.gz",
       RU = WORK_TRIM + "{sample}_2_trim.fastq.gz",
       html = WORK_QC + "{sample}.html",
       json = WORK_QC + "{sample}.json"

    priority: 40

    threads:
      8

    params:
      lenght=30

    shell:
      "fastp --thread {threads} --html {output.html} --json {output.json} -i {input.R1} -I {input.R2} -o {output.RP} -O {output.RU} -l {params.lenght} --adapter_fasta adapter.fa"


rule kallisto_index:
    input:
      WORK_KALL + "Homo_sapiens.GRCh38.cdna.all.fa"

    output:
      WORK_KALL + "Homo_sapiens.GRCh38.cdna.all.index"

    threads:
     8

    shell:
      "cp {input} {output} | kallisto index -i {output} {input}"


rule kallisto_quant:
    input:
      fq1 = WORK_TRIM + "{sample}_1_trim.fastq.gz",
      fq2 = WORK_TRIM + "{sample}_2_trim.fastq.gz",
      idx = WORK_KALL + "Homo_sapiens.GRCh38.cdna.all.index"

    output:
      WORK_KALL + "{sample}/abundance.tsv"

    params:
      outdir = WORK_KALL + "{sample}/"

    threads:
       8

    shell:
      "kallisto quant -i {input.idx} -o {params.outdir} -t {threads} {input.fq1} {input.fq2}"