analysis-workflows/definitions/subworkflows/molecular_alignment.cwl at 05bb4e148bcc0c02c3d8d3fced6818e5298a1a3d · genome/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
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
label: "umi molecular alignment workflow"
requirements:
    - class: SubworkflowFeatureRequirement
    - class: ScatterFeatureRequirement
inputs:
    bam:
        type: File[]
    sample_name:
        type: string
    read_structure:
        type: string[]
    reference:
        type:
            - string
            - File
        secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
    target_intervals:
       type: File?
    min_reads:
       type: int[]
       default: [1]
    max_read_error_rate:
       type: float?
       default: 0.05
    max_base_error_rate:
       type: float?
       default: 0.1
    min_base_quality:
       type: int
       default: 1
    max_no_call_fraction:
       type: float
       default: 0.5
outputs:
    umi_aligned_bam:
        type: File
        secondaryFiles: [.bai, ^.bai]
        outputSource: umi_index_bam/indexed_bam
    grouped_aligned_bam:
        type: File
        secondaryFiles: [.bai, ^.bai]
        outputSource: grouped_index_bam/indexed_bam
    consensus_aligned_bam:
        type: File
        secondaryFiles: [.bai, ^.bai]
        outputSource: consensus_index_bam/indexed_bam
    adapter_histogram:
        type: File[]
        outputSource: align/adapter_metrics
    duplex_seq_metrics:
        type: File[]
        outputSource: collect_duplex_seq_metrics/duplex_seq_metrics
steps:
    align:
        scatter: bam
        run: umi_alignment.cwl
        in:
            bam: bam
            read_structure: read_structure
            reference: reference
        out:
            [aligned_bam, adapter_metrics]
    merge:
        run: ../tools/merge_bams.cwl
        in:
            bams: align/aligned_bam
        out:
            [merged_bam]
    group_reads_by_umi:
        run: ../tools/group_reads.cwl
        in:
            bam: merge/merged_bam
        out:
            [grouped_bam]
    grouped_clip_overlap:
        run: ../tools/clip_overlap.cwl
        in:
            bam: group_reads_by_umi/grouped_bam
            reference: reference
        out:
            [clipped_bam]
    call_molecular_consensus:
        run: ../tools/call_molecular_consensus.cwl
        in:
            bam: group_reads_by_umi/grouped_bam
        out:
            [consensus_bam]
    align_consensus:
        run: ../tools/realign.cwl
        in:
            bam: call_molecular_consensus/consensus_bam
            reference: reference
        out:
            [consensus_aligned_bam]
    filter_consensus:
        run: ../tools/filter_consensus.cwl
        in:
            bam: align_consensus/consensus_aligned_bam
            reference: reference
            min_reads: min_reads
            max_read_error_rate: max_read_error_rate
            max_base_error_rate: max_base_error_rate
            min_base_quality: min_base_quality
            max_no_call_fraction: max_no_call_fraction
        out:
            [filtered_bam]
    consensus_clip_overlap:
        run: ../tools/clip_overlap.cwl
        in:
            bam: filter_consensus/filtered_bam
            reference: reference
        out:
            [clipped_bam]
    collect_duplex_seq_metrics:
       run: ../tools/duplex_seq_metrics.cwl
       in:
            bam: group_reads_by_umi/grouped_bam
            intervals: target_intervals
            description: sample_name
       out:
            [duplex_seq_metrics]
    umi_index_bam:
        run: ../tools/index_bam.cwl
        in:
            bam: merge/merged_bam
        out:
            [indexed_bam]
    grouped_index_bam:
        run: ../tools/index_bam.cwl
        in:
            bam: grouped_clip_overlap/clipped_bam
        out:
            [indexed_bam]
    consensus_index_bam:
        run: ../tools/index_bam.cwl
        in:
            bam: consensus_clip_overlap/clipped_bam
        out:
            [indexed_bam]