-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathnextflow.config
205 lines (174 loc) · 8.13 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
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
umcugenetics/dxnextflowrna Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Metadata sequencers
seq_platform = 'Illumina'
seq_center = 'UMCU Genetics'
// Input options
input = null
// References
// Homo_sapiens GRCh38 GCA_000001405.15
gencode_version_name = "GRCh38_gencode_v22_CTAT_lib_Mar012021"
genome_base = "/hpc/diaggen/data/databases/ref_genomes/${params.gencode_version_name}/${params.gencode_version_name}.plug-n-play/ctat_genome_lib_build_dir"
fasta = "${params.genome_base}/ref_genome.fa"
fai = "${params.genome_base}/ref_genome.fa.fai"
gtf = "${params.genome_base}/ref_annot.gtf"
star_index = "${params.genome_base}/ref_genome.fa.star.idx/"
// Dx_tracks references
dx_tracks_path = '/hpc/diaggen/software/development/Dx_tracks/'
// Custom reference files GRCh38
gene_bed = "${params.dx_tracks_path}/rna/${params.gencode_version_name}.ref_annot.gtf.bed"
ref_flat = "${params.dx_tracks_path}/rna/${params.gencode_version_name}.ref_annot.gtf.refflat"
rrna_intervals = "${params.dx_tracks_path}/rna/GRCh38_rRNA_genbank.interval_list"
// Reference files sortmerna
rrna_database_manifest = "${projectDir}/assets/sortmerna-db-default.txt"
sortmerna_index = "/hpc/diaggen/data/databases/sortmerna/sortmerna_index/genome/sortmerna/idx"
sortmerna_index_versions = "/hpc/diaggen/data/databases/sortmerna/sortmerna_index/genome/sortmerna/versions.yml"
save_non_ribo_reads = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Output / Boilerplate options
outdir = null
analysis_id = null
publish_dir_mode = 'link'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
cluster_options = "--mail-user ${params.email} --mail-type FAIL --account=diaggen"
// Tool arguments
rseqc_modules = "bam_stat,infer_experiment,inner_distance,junction_annotation,junction_saturation,read_distribution,read_duplication"
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
executor {
queueSize = 1000
pollInterval = '1min'
queueStatInterval = '5min'
submitRatelimit = '10sec'
}
mail {
smtp.host = 'localhost'
}
profiles {
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
singularity.runOptions = '-B /hpc:/hpc -B $TMPDIR:$TMPDIR'
singularity.cacheDir = '/hpc/diaggen/software/singularity_cache/'
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
cacheDir = '/hpc/diaggen/software/singularity_cache/'
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load umcugenetics/dxnextflowrna custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/dxnextflowrna.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
singularity.registry = 'quay.io'
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// 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 = "${params.outdir}/log/nextflow_timeline.html"
overwrite = true
}
report {
enabled = true
file = "${params.outdir}/log/nextflow_report.html"
overwrite = true
}
trace {
enabled = true
file = "${params.outdir}/log/nextflow_trace.txt"
fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt'
overwrite = true
}
manifest {
name = 'umcugenetics/dxnextflowrna'
author = """UMCU Genetics"""
homePage = 'https://github.com/umcugenetics/dxnextflowrna'
description = """UMCU Genetics RNA seq Workflow"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.10.2'
version = '1.0.0'
doi = ''
}
// Nextflow plugins
plugins {
id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input <INPUTDIR> --outdir <OUTDIR> --analysis_id <analysis_id>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/${manifest.name}/blob/master/CITATIONS.md
"""
}
summary {
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'