tempo/containers/multiqc/example_exome_multiqc_config.yaml at f5667fa177ab27f510674f355b990128b2672dfe · mskcc/tempo · 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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
custom_logo: 'tempoLogo.png'
custom_logo_title: 'CCS - Tempo'

show_analysis_paths: False

report_header_info:
    - Analysis Workflow: Tempo
    - Assay Type: 'Exome'
    - Sequencing Platform: 'Illumina Hiseq'
    - Sequencing Setup: '2x100'
custom_data:
    genstatsconpair:
        plot_type: 'generalstats'
        pconfig:
            - Tumor:
                hidden: True
            - Normal:
                hidden: False
            - Tumor_Contamination:
                hidden: False
            - Normal_Contamination:
                hidden: False
            - Concordance:
                hidden: False
    conpair:
        file_format: 'tsv'
        section_name: 'Conpair T-N Results'
        description: 'Concordance and contamination estimations for tumor–normal pairs as performed by customized version of Conpair'
        plot_type: 'table'
        pconfig:
            id: 'conpair_table'
            namespace: 'Concordance_estimates'
    alfredrg:
        file_format: 'tsv'
        section_name: 'Alfred RG-Aware Mapping Quality'
        description: 'Sample mapping quality with respect to read group'
        plot_type: 'linegraph'
        pconfig:
            id: 'alfred_rgY_mapping_linegraph'
            title: 'Per read-group Mapping Quality'
            ylab: 'Fraction of Reads'
            xlab: 'Mapping Quality'
    alfred:
        file_format: 'tsv'
        section_name: 'Alfred RG-Unaware Mapping Quality'
        description: 'Sample mapping quality without respect to read group'
        plot_type: 'linegraph'
        pconfig:
            id: 'alfred_rgN_mapping_linegraph'
            title: 'Per-sample Sample Mapping Quality'
            ylab: 'Fraction of Reads'
            xlab: 'Mapping Quality'
    genstats-QCStatus:
        plot_type: 'generalstats'
        pconfig:
            - Status:
                hidden: False
            - Reason:
                hidden: False
    QCStatus:
        plot_type: 'table'
        pconfig:
            - Status:
                hidden: False
            - Reason:
                hidden: False
    facets_qc:
        file_format: 'tsv'
        section_name: 'Facets QC'
        description: 'Results from Facets QC'
        plot_type: 'table'
        pconfig:
            id: 'facets_qc'
            namespace: 'facets_qc'
    facets_summary:
        file_format: 'tsv'
        section_name: 'Facets Run Summary'
        description: 'Results from Facets'
        plot_type: 'table'
        pconfig:
            id: 'facets_summary'
            namespace: 'facets_summary_report'
sp:
    genstatsconpair:
        fn: 'conpair_genstat.tsv'
    conpair:
        fn: 'conpair.tsv'
    alfredrg:
        fn: '*.rgY.MQ.alfred.tsv'
    alfred:
        fn: '*.rgN.MQ.alfred.tsv'
    genstats-QCStatus:
        fn: "genstats-QC_Status.txt"
    QCStatus:
        fn: "QC_Status.txt"
    facets_qc:
        fn: "*.qc.txt"
        contents: "mafr_median_clonal"
    facets_summary:
        fn: "*_OUT.txt"
        contents: "purity_cval"

table_cond_formatting_rules:
    mqc-generalstats-genstatsconpair-Tumor_Contamination:
        pass:
            - lt: 1
            - eq: 1
        warn:
            - gt: 1
        fail:
            - gt: 5
    mqc-generalstats-genstatsconpair-Normal_Contamination:
        pass:
            - lt: 1
            - eq: 1
        warn:
            - gt: 1
        fail:
            - gt: 5
    mqc-generalstats-genstatsconpair-Concordance:
        pass:
            - gt: 90
            - eq: 90
        warn:
            - lt: 90
        fail:
            - lt: 75
    Tumor_Contamination:
        pass:
            - lt: 1
            - eq: 1
        warn:
            - gt: 1
        fail:
            - gt: 5
    Normal_Contamination:
        pass:
            - lt: 1
            - eq: 1
        warn:
            - gt: 1
        fail:
            - gt: 5
    Concordance:
        pass:
            - gt: 90
            - eq: 90
        warn:
            - lt: 90
        fail:
            - lt: 75
    mqc-generalstats-picard-FOLD_ENRICHMENT:
        pass:
            - gt: 45
            - eq: 45
        warn:
            - lt: 45
        fail:
            - lt: 30
    FOLD_ENRICHMENT:
        pass:
            - gt: 45
            - eq: 45
        warn:
            - lt: 45
        fail:
            - lt: 30
    mqc-generalstats-picard-PCT_TARGET_BASES_50X:
        pass:
            - gt: 75
            - eq: 75
        warn:
            - lt: 75
    PCT_PF_UQ_READS_ALIGNED:
        pass:
            - gt: 60
            - eq: 60
        warn:
            - lt: 60
        fail:
            - lt: 40
    dipLogR_flag:
        fail:
            - s_eq: 'turnoff'
    wgd:
        fail:
            - s_eq: 'turnoff'

table_cond_formatting_colours:
    - pass: '#5cb85c'
    - warn: '#f0ad4e'
    - fail: '#d9534f'

picard_config:
    HsMetrics_table_cols:
        - MEAN_TARGET_COVERAGE
        - MEAN_BAIT_COVERAGE
        - ZERO_CVG_TARGETS_PCT
        - FOLD_ENRICHMENT
        - PCT_TARGET_BASES_50X
        - PCT_TARGET_BASES_30X
        - AT_DROPOUT
        - GC_DROPOUT
    HsMetrics_table_cols_hidden:
        - ZERO_CVG_TARGETS_PCT
        - PF_READS
        - PF_UNIQUE_READS
        - PF_UQ_BASES_ALIGNED
    general_stats_target_coverage:
        - 30
        - 50
table_columns_visible:
    fastp: False