/
multiqc_config.yaml
executable file
·150 lines (142 loc) · 5.21 KB
/
multiqc_config.yaml
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
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/atacseq" target="_blank">nf-core/atacseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://github.com/nf-core/atacseq/blob/master/docs/output.md" target="_blank">documentation</a>.
data_format: 'yaml'
run_modules:
- custom_content
- fastqc
- cutadapt
- samtools
- picard
- preseq
- featureCounts
- deeptools
exclude_modules:
- 'general_stats'
module_order:
- fastqc:
name: 'LIB: FastQC (raw)'
info: 'This section of the report shows FastQC results before adapter trimming for individual libraries.'
path_filters:
- './fastqc/*.zip'
- cutadapt:
name: 'LIB: Cutadapt (trimmed)'
info: 'This section of the report shows the length of trimmed reads by Cutadapt for individual libraries.'
- fastqc:
name: 'LIB: FastQC (trimmed)'
info: 'This section of the report shows FastQC results after adapter trimming for individual libraries.'
path_filters:
- './trimgalore/fastqc/*.zip'
- samtools:
name: 'LIB: SAMTools'
info: 'This section of the report shows SAMTools results for individual libraries.'
path_filters:
- './alignment/library/*'
- samtools:
name: 'MERGED LIB: SAMTools (unfiltered)'
info: 'This section of the report shows SAMTools results after merging libraries and before filtering.'
path_filters:
- './alignment/mergedLibrary/*.mLb.mkD.sorted.bam*'
- preseq:
name: 'MERGED LIB: Preseq (unfiltered)'
info: 'This section of the report shows Preseq results after merging libraries and before filtering.'
- samtools:
name: 'MERGED LIB: SAMTools (filtered)'
info: 'This section of the report shows SAMTools results after merging libraries and after filtering.'
path_filters:
- './alignment/mergedLibrary/*.mLb.clN.sorted.bam*'
- picard:
name: 'MERGED LIB: Picard'
info: 'This section of the report shows picard results after merging libraries and after filtering.'
path_filters:
- './alignment/mergedLibrary/picard_metrics/*'
- deeptools:
name: 'MERGED LIB: deepTools'
anchor: 'mlib_deeptools'
info: 'This section of the report shows QC plots generated by deepTools.'
- featureCounts:
name: 'MERGED LIB: featureCounts'
anchor: 'mlib_featurecounts'
info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
path_filters:
- './macs/mergedLibrary/consensus/*.summary'
- samtools:
name: 'MERGED REP: SAMTools'
info: 'This section of the report shows SAMTools results after merging replicates and filtering.'
path_filters:
- './alignment/mergedReplicate/*'
- picard:
name: 'MERGED REP: Picard'
anchor: 'mrep_picard'
info: 'This section of the report shows picard results after merging libraries and before filtering.'
path_filters:
- './alignment/mergedReplicate/*'
- featureCounts:
name: 'MERGED REP: featureCounts'
anchor: 'mrep_featurecounts'
info: 'This section of the report shows featureCounts results for the number of reads assigned to merged replicate consensus peaks.'
path_filters:
- './macs/mergedReplicate/consensus/*.summary'
report_section_order:
mlib_peak_count:
before: mlib_deeptools
mlib_frip_score:
before: mlib_peak_count
mlib_peak_annotation:
before: mlib_frip_score
mlib_featurecounts:
before: mlib_peak_annotation
mlib_deseq2_pca:
before: mlib_featurecounts
mlib_deseq2_clustering:
before: mlib_deseq2_pca
mrep_peak_count:
before: mrep_picard
mrep_frip_score:
before: mrep_peak_count
mrep_peak_annotation:
before: mrep_frip_score
mrep_featurecounts:
before: mrep_peak_annotation
mrep_deseq2_pca:
before: mrep_featurecounts
mrep_deseq2_clustering:
before: mrep_deseq2_pca
software_versions:
order: -1001
nf-core-atacseq-summary:
order: -1002
custom_plot_config:
picard_insert_size:
cpswitch_c_active: False
smooth_points: 1000
featurecounts:
cpswitch_c_active: False
featurecounts-1:
cpswitch_c_active: False
extra_fn_clean_exts:
- 'fastq.gz'
- '_trimmed'
- '_val'
- 'sorted.bam'
- '.Lb'
- 'mkD'
- 'clN'
- 'mLb'
- 'mRp'
- '_peaks'
# # Customise the module search patterns to speed up execution time
# # - Skip module sub-tools that we are not interested in
# # - Replace file-content searching with filename pattern searching
# # - Don't add anything that is the same as the MultiQC default
# # See https://multiqc.info/docs/#optimise-file-search-patterns for details
sp:
cutadapt:
fn: '*trimming_report.txt'
preseq:
fn: '*.ccurve.txt'
deeptools/plotFingerprintOutRawCounts:
fn: '*plotFingerprint*'
deeptools/plotProfile:
fn: '*plotProfile*'