forked from nf-core/rnasplice
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow.config
397 lines (360 loc) · 13.8 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
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/rnasplice Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
contrasts = null
source = 'fastq'
// References
genome = null
transcript_fasta = null
gtf_extra_attributes = 'gene_name'
gtf_group_features = 'gene_id'
gencode = false
save_reference = false
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
// Trimming
clip_r1 = null
clip_r2 = null
three_prime_clip_r1 = null
three_prime_clip_r2 = null
trim_nextseq = null
save_trimmed = false
skip_trimming = false
skip_trimgalore_fastqc = false
min_trimmed_reads = 10000
// Alignment
aligner = 'star_salmon'
pseudo_aligner = 'salmon'
bam_csi_index = false
seq_center = null
salmon_quant_libtype = null
star_ignore_sjdbgtf = false
skip_alignment = false
save_unaligned = false
save_align_intermeds = false
save_merged_fastq = false
// QC
skip_bigwig = true
skip_fastqc = false
// rMATs
rmats = true
rmats_splice_diff_cutoff = 0.0001
rmats_paired_stats = true
rmats_read_len = 40
rmats_novel_splice_site = false
rmats_min_intron_len = 50
rmats_max_exon_len = 500
// DEXSeq DEU
dexseq_exon = true
save_dexseq_annotation = false
gff_dexseq = null
alignment_quality = 10
aggregation = true
save_dexseq_plot = true
n_dexseq_plot = 10
// edgeR DEU
edger_exon = true
save_edger_plot = true
n_edger_plot = 10
// DEXSeq DTU
dexseq_dtu = true
dtu_txi = 'dtuScaledTPM'
// Miso
sashimi_plot = true
miso_genes = 'ENSG00000004961, ENSG00000005302, ENSG00000147403'
miso_genes_file = null
miso_read_len = 75
fig_width = 7
fig_height = 7
// DRIMSeq Filtering
min_samps_feature_expr = 2
min_samps_feature_prop = 2
min_samps_gene_expr = 4
min_feature_expr = 10
min_feature_prop = 0.1
min_gene_expr = 10
// SUPPA options
suppa = true
suppa_per_local_event = true
suppa_per_isoform = true
suppa_tpm = null
// SUPPA Generate events options
generateevents_pool_genes = true
generateevents_event_type = 'SE SS MX RI FL'
generateevents_boundary = 'S'
generateevents_threshold = 10
generateevents_exon_length = 100
psiperevent_total_filter = 0
// SUPPA Diffsplice options
diffsplice_local_event = true
diffsplice_isoform = true
diffsplice_method = 'empirical'
diffsplice_area = 1000
diffsplice_lower_bound = 0
diffsplice_gene_correction = true
diffsplice_paired = true
diffsplice_alpha = 0.05
diffsplice_median = false
diffsplice_tpm_threshold = 0
diffsplice_nan_threshold = 0
// SUPPA Cluster options
clusterevents_local_event = true
clusterevents_isoform = true
clusterevents_sigthreshold = null
clusterevents_dpsithreshold= 0.05
clusterevents_eps = 0.05
clusterevents_metric = 'euclidean'
clusterevents_separation = null
clusterevents_min_pts = 20
clusterevents_method = 'DBSCAN'
// 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
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/rnasplice custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/rnasplice.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/rnasplice profiles: ${params.custom_config_base}/pipeline/rnasplice.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
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_edger { includeConfig 'conf/test_edger.config' }
test_rmats { includeConfig 'conf/test_rmats.config' }
test_dexseq { includeConfig 'conf/test_dexseq.config' }
test_suppa { includeConfig 'conf/test_suppa.config' }
test_fastq { includeConfig 'conf/test_fastq.config' }
test_genome_bam { includeConfig 'conf/test_genome_bam.config' }
test_transcriptome_bam { includeConfig 'conf/test_transcriptome_bam.config' }
test_salmon_results { includeConfig 'conf/test_salmon_results.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
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// 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 = 'nf-core/rnasplice'
author = """Ben Southgate, James Ashmore"""
homePage = 'https://github.com/nf-core/rnasplice'
description = """Alternative splicing analysis using RNA-seq."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0.4'
doi = '10.5281/zenodo.8424632'
}
// 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
}
}
}