-
Notifications
You must be signed in to change notification settings - Fork 0
/
template.config
149 lines (126 loc) · 7.6 KB
/
template.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
includeConfig "${projectDir}/config/default.config"
includeConfig "${projectDir}/config/methods.config"
includeConfig "${projectDir}/nextflow.config"
params {
input_csv = '' // Path to input CSV if inputs are being given through CSV; if using YAML inputs, remove this parameter from the config
output_dir = ''
leading_work_dir = '' //Should be a /hot/path | Can't use /scratch
pipeline_work_dir = '/scratch' //For individual pipeline outputs before copying to output_dir
project_id = ''
save_intermediate_files = false // Metapipeline-level intermediate files
// If specified, an email will be sent to this address for every pipeline
// start and completion
status_email_address = ""
partition = 'F72'
clusterOptions = '--exclusive'
max_parallel_jobs = 5
// How long to wait between job submissions, in minutes. Default: 90
// If WGS mode below is enabled, the interval will be replaced by the defaults for WGS mode and WGS queue
cluster_submission_interval = 90
// Whether to run samples in WGS queue with WGS rate limit
// Disable for non-WGS samples
uclahs_cds_wgs = true
sample_mode = 'paired' // Choose from: 'single', 'paired', 'multi'
// Select pipeline(s) to run. Choices: 'align-DNA', 'recalibrate-BAM', 'generate-SQC-BAM', 'calculate-targeted-coverage', 'call-gSNP', 'call-mtSNV', 'call-sSNV', 'call-sSV', 'call-gSV', 'call-sCNA'
requested_pipelines = ['align-DNA', 'recalibrate-BAM', 'generate-SQC-BAM', 'call-gSNP', 'call-mtSNV', 'call-sSNV', 'call-sSV', 'call-gSV', 'call-sCNA']
// Override conversion to FASTQ and re-alignment with BAM input
override_realignment = false
// Override recalibrate-BAM
override_recalibrate_bam = false
/**
Targeted mode options
When targeted-coverage is enabled, control whether the original provided intervals for the pipelines should be used
By default, with this option disabled, the expanded intervals from targeted-coverage will be used
*/
use_original_intervals = false
// Pipeline-specific params under each respective pipeline
pipeline_params {
convert_BAM2FASTQ {
get_bam_stats_SAMtools_cpus = 8
collate_bam_SAMtools_cpus = 8
// Uncomment to set read group tag values to override that from the original BAMs.
// This can also be usful if you know your BAM files don't have those tags.
// sequencing_center =
// platform_unit =
// id_for_pu =
}
align_DNA {
enable_spark = true
mark_duplicates = true
reference_fasta_bwa = '/hot/resource/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/alt-aware/genome.fa'
aligner = ['BWA-MEM2']
}
recalibrate_BAM {
aligner = "BWA-MEM2-2.2.1"
reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
bundle_mills_and_1000g_gold_standard_indels_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
bundle_known_indels_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz"
bundle_v0_dbsnp138_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz"
bundle_contest_hapmap_3p3_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz"
parallelize_by_chromosome = true
}
calculate_targeted_coverage {
reference_dict = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict'
reference_dbSNP = '/hot/resource/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz'
genome_sizes = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai'
target_bed = 'path/to/target/bedfile' //required
bait_bed = '' //optional, path/to/bait/bedfile
collect_metrics = true // whether or not to calculate coverage metrics
off_target_depth = true //whether or not to calculate depth at off-target dbSNP loci
output_enriched_target_file = true // whether or not to output a new target file containing high-coverage off-target dbSNP loci
target_depth = false // whether or not to calculate per-base depth in target regions
}
generate_SQC_BAM {
algorithms = ['stats', 'collectwgsmetrics']
reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
}
call_gSNP {
reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
bundle_mills_and_1000g_gold_standard_indels_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
bundle_v0_dbsnp138_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz"
bundle_hapmap_3p3_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz"
bundle_omni_1000g_2p5_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz"
bundle_phase1_1000g_snps_high_conf_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
}
call_sSNV {
algorithm = ['somaticsniper', 'strelka2', 'mutect2', 'muse']
reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
exome = false
intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
ncbi_build = 'GRCh38'
}
call_mtSNV {
mt_ref_genome_dir = '/hot/resource/mitochondria_ref/genome_fasta/'
gmapdb = '/hot/resource/mitochondria_ref/gmapdb/gmapdb_2021-03-08/'
}
call_gSV {
reference_fasta = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
exclusion_file = '/hot/resource/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv'
mappability_map = '/hot/resource/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz'
}
call_sSV {
algorithm = ['delly', 'manta']
reference_fasta = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
exclusion_file = '/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv'
}
call_sCNA {
algorithm = ['battenberg', 'cnv_facets']
sample_sex = "male"
position_scale = "genome-position"
dbSNP_file = "/hot/resource/tool-specific-input/RecSNV/GRCh38/dbsnp_b150_grch38.vcf.gz"
battenberg_reference = "/hot/resource/tool-specific-input/Battenberg/download_202204/GRCh38/battenberg_ref_hg38_chr/"
reference_dict = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict"
}
call_SRC {
SRC = [
[
algorithm: 'PyClone-VI',
options: ''
]
]
}
}
}
methods.set_up()