-
Notifications
You must be signed in to change notification settings - Fork 3
/
nextflow.config
179 lines (172 loc) · 4.34 KB
/
nextflow.config
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
profiles {
docker {
process {
withName: nextclade {
container = 'nextstrain/nextclade:latest'
}
withName: pangolin {
container = 'staphb/pangolin:latest'
}
withName: lineage_assignment {
container = 'ufuomababatunde/bammix:v1.1.0'
}
withName: bammix {
container = 'ufuomababatunde/bammix:v1.1.0'
}
withName: bam_filter {
container = 'pegi3s/samtools_bcftools:latest'
}
withName: virstrain {
container = 'lanadelrea/virstrain:latest'
}
withName: virstrain_summary {
container = 'ufuomababatunde/bammix:v1.1.0'
}
withName: freyja {
container = 'staphb/freyja:latest'
}
withName: freyja_demix {
container = 'staphb/freyja:latest'
}
withName: freyja_aggregate {
container = 'staphb/freyja:latest'
}
withName: freyja_plot {
container = 'staphb/freyja:latest'
}
withName: makevcf {
container = 'pegi3s/samtools_bcftools:latest'
}
withName: bammixplot {
container = 'ufuomababatunde/bammix:v1.1.0'
}
withName: aafplot_mutations {
container = 'ufuomababatunde/bammix:v1.1.0'
}
withName: aafplot_amplicons {
container = 'ufuomababatunde/bammix:v1.1.0'
}
withName: ampliconsorting_DeltaReads {
container = 'lindenb/jvarkit:1b2aedf24'
}
withName: ampliconsorting_OmicronReads {
container = 'lindenb/jvarkit:1b2aedf24'
}
withName: ampliconsorting_samtools {
container = 'pegi3s/samtools_bcftools:latest'
}
withName: ampliconsorting_bgzip {
container = 'vandhanak/bcftools:1.3.1'
}
withName: ampliconsorting_fasta {
container = 'pegi3s/samtools_bcftools:latest'
}
withName: ampliconsorting_lineageAssignment_Pangolin {
container = 'staphb/pangolin:latest'
}
withName: ampliconsorting_lineageAssignment_Nextclade {
container = 'nextstrain/nextclade:latest'
}
withName: report {
container = 'ufuomababatunde/rmarkdown:1.1.0'
}
}
}
conda {
process {
withName: nextclade {
conda = 'Katmon/envs/nextclade.yml'
}
withName: pangolin {
conda = 'Katmon/envs/pangolin.yml'
}
withName: lineage_assignment {
conda = 'Katmon/envs/bammix.yml'
}
withName: bammix {
conda = 'Katmon/envs/bammix.yml'
}
withName: bam_filter {
conda = 'Katmon/envs/samtools_bcftools.yml'
}
withName: virstrain {
conda = 'Katmon/envs/virstrain.yml'
}
withName: virstrain_summary {
conda = 'Katmon/envs/bammix.yml'
}
withName: freyja {
conda = 'Katmon/envs/freyja.yml'
}
withName: freyja_demix {
conda = 'Katmon/envs/freyja.yml'
}
withName: freyja_aggregate {
conda = 'Katmon/envs/freyja.yml'
}
withName: freyja_plot {
conda = 'Katmon/envs/freyja.yml'
}
withName: makevcf {
conda = 'Katmon/envs/samtools_bcftools.yml'
}
withName: bammixplot {
conda = 'Katmon/envs/bammix.yml'
}
withName: aafplot_mutations {
conda = 'Katmon/envs/bammix.yml'
}
withName: aafplot_amplicons {
conda = 'Katmon/envs/bammix.yml'
}
withName: ampliconsorting_DeltaReads {
conda = 'Katmon/envs/jvarkit.yml'
}
withName: ampliconsorting_OmicronReads {
conda = 'Katmon/envs/jvarkit.yml'
}
withName: ampliconsorting_samtools {
conda = 'Katmon/envs/samtools_bcftools.yml'
}
withName: ampliconsorting_bgzip {
conda = 'Katmon/envs/samtools_bcftools.yml'
}
withName: ampliconsorting_fasta {
conda = 'Katmon/envs/samtools_bcftools.yml'
}
withName: ampliconsorting_lineageAssignment_Pangolin {
conda = 'Katmon/envs/pangolin.yml'
}
withName: ampliconsorting_lineageAssignment_Nextclade {
conda = 'Katmon/envs/nextclade.yml'
}
withName: report {
conda = 'Katmon/envs/rmarkdown.yml'
}
}
}
}
docker {
enabled = true
temp = 'auto'
}
conda {
enabled = true
temp = 'auto'
runOptions = '-u $(id -u):(id g)'
}
params {
reference = "${baseDir}/assets/sars-cov-2/reference-sequence.fasta"
SC2_dataset = "${baseDir}/assets/sars-cov-2"
jvarkit_jar = "${baseDir}/bin/jvarkit.jar"
sort_delta_reads = "${baseDir}/bin/sort_delta_reads.js"
sort_omicron_reads = "${baseDir}/bin/sort_omicron_reads.js"
report_rmd = "${baseDir}/bin/summary-report.Rmd"
report_rmd_no_bammix = "${baseDir}/bin/summary-report-no-bammix.Rmd"
}
process {
withName: 'freyja_demix' {
memory = '8 GB'
cpus = 2
}
}