-
Notifications
You must be signed in to change notification settings - Fork 1
/
nextflow.config
355 lines (301 loc) · 13.7 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
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mycobactopia-org/MTBseq-nf Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
input = null// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
// Subworkflows
only_qc = false
parallel = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
//-------------------------------------
// OPTIONS FROM MTBSEQ MANUAL
//-------------------------------------
// Hidden parameters
user = "root"
mtbseq_path = "MTBseq"
// Name of the project and the analysis
cohort_tsv = null
project = "mtbseqnf"
// Setting this OPTION will add an additional filter that excludes all variants except SNPs.
snp_vars = false
// Setting this OPTION has major implications on how the mapping data for each position is processed. By default, the majority allele is called and taken for further calculations.
// If the --lowfreq_vars OPTION is set, MTBseq will consider the majority allele distinct from wild type, if such an allele is present.
// This means that only in this detection mode, MTBseq will report variants present only in subpopulations, i.e. low frequency mutations.
// Of course, OPTIONS --mincovf, --mincovr, --minphred and --minfreq need to be set accordingly.
// Please be aware that output generated in this detection mode should not be used for phylogenetic analysis.
lowfreq_vars = false
// The OPTION sets a threshold for the sequence data quality to be used for the mpileup creation
minbqual = 13
// The OPTION sets a minimum forward read coverage threshold. Alleles must have a forward coverage of this VALUE or higher to be considered.
mincovf = 4
// The OPTION sets a minimum reverse read coverage threshold. Alleles must have a reverse coverage of this VALUE or higher to be considered.
mincovr = 4
// The OPTION sets a minimum number of reads indicating an allele with a phred score of at least 20.
minphred = 4
// The OPTION sets a minimum frequency for an allele.
minfreq = 75
// The option sets a minimum percentage of samples with unambiguous information for position.
unambig = 95
// The OPTION sets a window size in which the algorithm scans for the occurrence of multiple variants within the same sample.
// If more than one variant occurs within this window in the same sample, the positions will be excluded.
window = 12
// The OPTION sets a SNP distance that is used to classify samples into groups of samples, using agglomerative clustering.
// If SNP distances between samples are less or equal this VALUE, they are grouped together.
distance = 12
// The OPTION sets the maximum number of CPUs to use within the pipeline.
// You can use more than one core in order to execute the pipeline faster. 8 is the current maximum.
threads = 8
ref_and_indexes_path = "${projectDir}/data/references/ref/"
//--------------
//
//TODO: Described in https://github.com/mtb-bioinformatics/mtbseq-nf/issues/53
// --ref This OPTION sets the reference genome for the read mapping.
// By default, the genome of Mycobacterium tuberculosis H37Rv (NC_000962.3) is set as reference.
// User supplied FASTA files for other reference genomes should be placed in the directory /MTBseq_source/var/ref/, and the respective name given without .fasta extension.
// This OPTION sets the reference genome for the read mapping.
// ref = "${params.ref_and_indexes_path}/M._tuberculosis_H37Rv_2015-11-13.fasta"
//--------------
// This OPTION sets a list of known variant positions associated to drug resistance for resistance prediction.
resilist = "${projectDir}/data/references/res/MTB_Resistance_Mediating.txt"
// This OPTION sets a list of interesting regions to be used for annotation of detected variants
intregions = "${projectDir}/data/references/res/MTB_Extended_Resistance_Mediating.txt"
// This OPTION specifies a gene categories file to annotate essential and non-essential genes as well as repetitive regions. SNPs in repetitive regions will be excluded for phylogenetic analysis.
categories = "${projectDir}/data/references/cat/MTB_Gene_Categories.txt"
// This OPTION specifies a file for base quality recalibration. The list must be in VCF format and should contain known SNPs.
basecalib = "${projectDir}/data/references/res/MTB_Base_Calibration_List.vcf"
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load mycobactopia-org/MTBseq-nf custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/mtbseqnf.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/mtbseqnf profiles: ${params.custom_config_base}/pipeline/mtbseqnf.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_publication { includeConfig 'conf/test_publication.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'mycobactopia-org/MTBseq-nf'
author = """Abhinav Sharma (@abhi18av) and Davi Marcon (@mxrcon)"""
homePage = 'https://github.com/mycobactopia-org/MTBseq-nf'
description = """`MTBseq-nf` pipeline makes [MTBseq](https://github.com/ngs-fzb/MTBseq_source) simple and easy to use via [Nextflow](https://www.nextflow.io/) workflow manager."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0'
doi = '10.5281/zenodo.5498063'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}