analysis-workflows/pipeline.cwl at master · dufeiyu/analysis-workflows · 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
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: "somatic pipeline"
requirements:
    - class: SubworkflowFeatureRequirement
inputs:
    reference:
        type: File
        secondaryFiles: [.fai, .bwt, .sa, .ann, .amb, .pac, ^.dict, .alt]
    normal_bams:
         type: File[]
    normal_readgroups:
          type: string[]
    tumor_bams:
         type: File[]
    tumor_readgroups:
          type: string[]
    mills:
        type: File
        secondaryFiles: [.tbi]
    known_indels:
        type: File
        secondaryFiles: [.tbi]
    dbsnp:
        type: File
        secondaryFiles: [.tbi]
    interval_list:
        type: File
    strelka_exome_mode:
        type: boolean
    cosmic_vcf:
        type: File?
        secondaryFiles: [.tbi]
outputs:
    final_vcf:
        type: File
        outputSource: detect_variants/final_vcf
        secondaryFiles: [.tbi]
steps:
    align_normal:
        run: unaligned_bam_to_bqsr/workflow.cwl
        in:
            bams: normal_bams
            readgroups: normal_readgroups
            reference: reference
            dbsnp: dbsnp
            mills: mills
            known_indels: known_indels
        out:
            [final_bam]
    align_tumor:
        run: unaligned_bam_to_bqsr/workflow.cwl
        in:
            bams: tumor_bams
            readgroups: tumor_readgroups
            reference: reference
            dbsnp: dbsnp
            mills: mills
            known_indels: known_indels
        out:
            [final_bam]
    detect_variants:
        run: detect_variants/detect_variants.cwl
        in:
            reference: reference
            tumor_bam: align_tumor/final_bam
            normal_bam: align_normal/final_bam
            interval_list: interval_list
            strelka_exome_mode: strelka_exome_mode
            dbsnp_vcf: dbsnp
            cosmic_vcf: cosmic_vcf
        out:
            [final_vcf]