-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow.config
192 lines (146 loc) · 3.67 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
180
181
182
183
184
185
186
187
188
189
190
191
192
params {
// WORKFLOW PARAMETERS TO REVIEW AT EACH RUN
// ----------------------------------------
// PacBio HiFi CCS FASTQ.gz file
pb_fastq = null
// Oxford Nanopore FASTQ.gz file
ont_fastq = null
// maximum size for split-up FASTQs (defaults to 100000)
split_max = 500000
// minimum number of reads required to run hifiasm with a given FASTQ
min_reads = 1000
// reference FASTA
ref_fasta = null
// desired regions sheet
desired_regions = null
// Where to place results
results = "$launchDir/results"
// whether to cleanup work directory after a successful run (defaults to false)
cleanup = false
// how many cpu cores to multithread across for each task
cpus = 6
// where to place the PacBio and ONT FASTQ for each extracted region
extracted = params.results + "/extracted_regions"
// where to place hifiasm results, including a FASTA of contigs
assembly = params.results + "/hifiasm_assembly"
}
// WHETHER TO GENERATE A REPORT OF RUN STATISTICS
report {
enabled = true
overwrite = true
file = "${params.results}/report.html"
}
// WHETHER TO GENERATE A VISUALIZATION OF THE WORKFLOW
dag {
enabled = true
overwrite = true
file = "${params.results}/workflow-visualization.png"
}
// WHETHER TO REMOVE TEMPORARY FILES AFTER A SUCCESSFUL RUN
cleanup = params.cleanup
// PROFILE OPTIONS
profiles {
standard {
docker.enabled = true
singularity.enabled = false
conda.enabled = false
process {
withLabel: "seqkit" {
container = "staphb/seqkit:2.8.1"
}
}
process {
withLabel: "map_and_extract" {
container = "dockerreg.chtc.wisc.edu/prall/map-and-extract:v1"
}
}
process {
withName:RUN_HIFIASM {
container = "dockerreg.chtc.wisc.edu/prall/hifiasm:29364"
}
}
}
docker {
docker.enabled = true
singularity.enabled = false
conda.enabled = false
process {
withName:MERGE_PACBIO_FASTQS {
container = "staphb/seqkit:2.8.1"
}
}
process {
withName:MERGE_ONT_FASTQS {
container = "staphb/seqkit:2.8.1"
}
}
process {
withLabel: "map_and_extract" {
container = "dockerreg.chtc.wisc.edu/prall/map-and-extract:v1"
}
}
process {
withLabel: "hifiasm" {
container = "dockerreg.chtc.wisc.edu/prall/hifiasm:29364"
}
}
}
singularity {
singularity.enabled = true
docker.enabled = false
conda.enabled = false
process {
withName:MERGE_PACBIO_FASTQS {
container = "docker://staphb/seqkit:2.8.1"
}
}
process {
withName:MERGE_ONT_FASTQS {
container = "docker://staphb/seqkit:2.8.1"
}
}
process {
withLabel: "map_and_extract" {
container = "docker://dockerreg.chtc.wisc.edu/prall/map-and-extract:v1"
}
}
process {
withLabel: "hifiasm" {
container = "docker://dockerreg.chtc.wisc.edu/prall/hifiasm:29364"
}
}
}
apptainer {
apptainer.enabled = true
docker.enabled = false
conda.enabled = false
process {
withName:MERGE_PACBIO_FASTQS {
container = "docker://staphb/seqkit:2.8.1"
}
}
process {
withName:MERGE_ONT_FASTQS {
container = "docker://staphb/seqkit:2.8.1"
}
}
process {
withLabel: "map_and_extract" {
container = "docker://dockerreg.chtc.wisc.edu/prall/map-and-extract:v1"
}
}
process {
withLabel: "hifiasm" {
container = "docker://dockerreg.chtc.wisc.edu/prall/hifiasm:29364"
}
}
}
}
// MANIFEST
manifest {
homePage = ''
mainScript = 'main.nf'
defaultBranch = 'main'
description = ''
author = ''
}