-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathLatency_PairedSingleSampleWf_optimized.inputs.json
executable file
·168 lines (161 loc) · 15.1 KB
/
Latency_PairedSingleSampleWf_optimized.inputs.json
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
{
"##_COMMENT1": "Take note of the .64 extensions on the reference files, issues between 32 and 64 bit OS",
"##_COMMENT2": "SAMPLES - read the README to find other examples.",
"PairedEndSingleSampleWorkflow.sample_name": "NA12878",
"PairedEndSingleSampleWorkflow.base_file_name": "NA12878",
"PairedEndSingleSampleWorkflow.flowcell_unmapped_bams": [
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HJYFJCCXX.4.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HJYFJCCXX.5.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HJYFJCCXX.6.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HJYFJCCXX.7.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HJYFJCCXX.8.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HJYN2CCXX.1.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.1.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.2.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.3.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.4.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.5.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.6.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.7.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35MCCXX.8.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35NCCXX.1.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK35NCCXX.2.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.1.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.2.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.3.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.4.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.5.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.6.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.7.Pond-492100.unmapped.bam",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/NA12878/bams/HK3T5CCXX.8.Pond-492100.unmapped.bam"
],
"PairedEndSingleSampleWorkflow.final_gvcf_name": "NA12878.g.vcf.gz",
"PairedEndSingleSampleWorkflow.unmapped_bam_suffix": ".unmapped.bam",
"##_COMMENT3": "REFERENCES",
"PairedEndSingleSampleWorkflow.fingerprint_genotypes_file": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/NA12878.hg38.reference.fingerprint.vcf",
"PairedEndSingleSampleWorkflow.contamination_sites_ud": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.contam.UD",
"PairedEndSingleSampleWorkflow.contamination_sites_bed": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.contam.bed",
"PairedEndSingleSampleWorkflow.contamination_sites_mu": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.contam.mu",
"PairedEndSingleSampleWorkflow.wgs_calling_interval_list": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/wgs_calling_regions.hg38.interval_list",
"PairedEndSingleSampleWorkflow.haplotype_scatter_count" : 50,
"PairedEndSingleSampleWorkflow.break_bands_at_multiples_of" : 100000,
"PairedEndSingleSampleWorkflow.ref_dict": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict",
"PairedEndSingleSampleWorkflow.ref_fasta": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
"PairedEndSingleSampleWorkflow.ref_fasta_index": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"PairedEndSingleSampleWorkflow.ref_alt": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
"PairedEndSingleSampleWorkflow.ref_sa": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
"PairedEndSingleSampleWorkflow.ref_amb": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
"PairedEndSingleSampleWorkflow.ref_bwt": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
"PairedEndSingleSampleWorkflow.ref_ann": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
"PairedEndSingleSampleWorkflow.ref_pac": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
"PairedEndSingleSampleWorkflow.known_snps_sites_vcf": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"PairedEndSingleSampleWorkflow.known_snps_sites_vcf_index": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"PairedEndSingleSampleWorkflow.dbSNP_vcf": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"PairedEndSingleSampleWorkflow.dbSNP_vcf_index": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"PairedEndSingleSampleWorkflow.wgs_coverage_interval_list": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/wgs_coverage_regions.hg38.interval_list",
"PairedEndSingleSampleWorkflow.wgs_evaluation_interval_list": "/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"PairedEndSingleSampleWorkflow.known_indels_sites_VCFs": [
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
],
"PairedEndSingleSampleWorkflow.known_indels_sites_indices": [
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"/mnt/lustre/genomics/wgs-data/data/RefArch_Broad_data/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
],
"##_COMMENT5": "PATH TO GENOMICS TOOLS FOR NON-DOCKERIZED WORKFLOW",
"PairedEndSingleSampleWorkflow.tool_path": "/mnt/lustre/genomics/tools",
"##_COMMENT6":"OPTIMIZATION FLAGS FOR BWA, SAMTOOLS, GATK-GKL",
"## SamToFastQ_COMMENT": "BWA mem is the bottleneck - request 48 cores for the task, assign 46T to bwa and let SamToFastQ and MergeBamAlignment use 1T each",
"PairedEndSingleSampleWorkflow.bwa_threads":4,
"## SamtoolsSort_COMMENT": "Threads for Samtools sort step",
"PairedEndSingleSampleWorkflow.samtools_threads":40,
"## GENERAL_COMMENT": "Compression level for all java commands",
"PairedEndSingleSampleWorkflow.compression_level":1,
"## HaplotypeCaller_MT_comment": "See comment in the WDL file",
"## HaplotypeCaller_pairHMM_comment": "Set to EXPERIMENTAL_FPGA_LOGLESS_CACHING if using FPGA",
"PairedEndSingleSampleWorkflow.gatk_gkl_pairhmm_implementation":"AVX_LOGLESS_CACHING",
"PairedEndSingleSampleWorkflow.gatk_gkl_pairhmm_threads":2,
"PairedEndSingleSampleWorkflow.HaplotypeCaller.smith_waterman_implementation":"AVX_ENABLED",
"PairedEndSingleSampleWorkflow.SortSampleBam.mem_limit": "5000M",
"##_COMMENT7":"JAVA HEAP MEMORY OPTIONS",
"PairedEndSingleSampleWorkflow.CollectQualityYieldMetrics.java_heap_memory_initial":"128m",
"PairedEndSingleSampleWorkflow.SamToFastqAndBwaMemAndMba.java_heap_memory_initial":"7300M",
"PairedEndSingleSampleWorkflow.SortSampleBam.java_heap_memory_initial":"201GB",
"PairedEndSingleSampleWorkflow.CollectUnsortedReadgroupBamQualityMetrics.java_heap_memory_initial":"5g",
"PairedEndSingleSampleWorkflow.CollectReadgroupBamQualityMetrics.java_heap_memory_initial":"5g",
"PairedEndSingleSampleWorkflow.CollectAggregationMetrics.java_heap_memory_initial":"5g",
"PairedEndSingleSampleWorkflow.CrossCheckFingerprints.java_heap_memory_initial":"2g",
"PairedEndSingleSampleWorkflow.CheckFingerprint.java_heap_memory_initial":"1g",
"PairedEndSingleSampleWorkflow.MarkDuplicates.java_heap_memory_initial":"4g",
"PairedEndSingleSampleWorkflow.BaseRecalibrator.java_heap_memory_initial":"3g",
"PairedEndSingleSampleWorkflow.GatherBqsrReports.java_heap_memory_initial":"3g",
"PairedEndSingleSampleWorkflow.ApplyBQSR.java_heap_memory_initial":"3g",
"PairedEndSingleSampleWorkflow.GatherBamFiles.java_heap_memory_initial":"2g",
"PairedEndSingleSampleWorkflow.ValidateBamFromCram.java_heap_memory_initial":"6g",
"PairedEndSingleSampleWorkflow.CollectWgsMetrics.java_heap_memory_initial":"2g",
"PairedEndSingleSampleWorkflow.CollectRawWgsMetrics.java_heap_memory_initial":"2g",
"PairedEndSingleSampleWorkflow.CalculateReadGroupChecksum.java_heap_memory_initial":"1g",
"PairedEndSingleSampleWorkflow.ScatterIntervalList.java_heap_memory_initial":"1g",
"PairedEndSingleSampleWorkflow.HaplotypeCaller.haplotypecaller_java_heap_memory_initial":"3600M",
"PairedEndSingleSampleWorkflow.MergeVCFs.java_heap_memory_initial":"2g",
"PairedEndSingleSampleWorkflow.ValidateGVCF.java_heap_memory_initial":"3g",
"PairedEndSingleSampleWorkflow.CollectGvcfCallingMetrics.java_heap_memory_initial":"2g",
"##_COMMENT8":"RUNTIME SECTION MEMORY OPTIONS",
"PairedEndSingleSampleWorkflow.CollectQualityYieldMetrics.memory":"2GB",
"PairedEndSingleSampleWorkflow.CheckFinalVcfExtension.memory":"2GB",
"PairedEndSingleSampleWorkflow.GetBwaVersion.memory":"1GB",
"PairedEndSingleSampleWorkflow.SamToFastqAndBwaMemAndMba.memory":"7300M",
"PairedEndSingleSampleWorkflow.SortSampleBam.memory":"201GB",
"PairedEndSingleSampleWorkflow.CollectUnsortedReadgroupBamQualityMetrics.memory":"7GB",
"PairedEndSingleSampleWorkflow.CollectReadgroupBamQualityMetrics.memory":"7GB",
"PairedEndSingleSampleWorkflow.CollectAggregationMetrics.memory":"7GB",
"PairedEndSingleSampleWorkflow.CrossCheckFingerprints.memory":"2GB",
"PairedEndSingleSampleWorkflow.CheckFingerprint.memory":"1GB",
"PairedEndSingleSampleWorkflow.MarkDuplicates.memory":"5GB",
"PairedEndSingleSampleWorkflow.CreateSequenceGroupingTSV.memory":"2GB",
"PairedEndSingleSampleWorkflow.BaseRecalibrator.memory":"3600M",
"PairedEndSingleSampleWorkflow.GatherBqsrReports.memory":"2GB",
"PairedEndSingleSampleWorkflow.ApplyBQSR.memory":"3500M",
"PairedEndSingleSampleWorkflow.GatherBamFiles.memory":"3GB",
"PairedEndSingleSampleWorkflow.ValidateBamFromCram.memory":"7GB",
"PairedEndSingleSampleWorkflow.CollectWgsMetrics.memory":"3GB",
"PairedEndSingleSampleWorkflow.CollectRawWgsMetrics.memory":"3GB",
"PairedEndSingleSampleWorkflow.CalculateReadGroupChecksum.memory":"2GB",
"PairedEndSingleSampleWorkflow.CheckContamination.memory":"2GB",
"PairedEndSingleSampleWorkflow.ScatterIntervalList.memory":"2GB",
"PairedEndSingleSampleWorkflow.HaplotypeCaller.memory":"3600M",
"PairedEndSingleSampleWorkflow.MergeVCFs.memory":"3GB",
"PairedEndSingleSampleWorkflow.ValidateGVCF.memory":"4GB",
"PairedEndSingleSampleWorkflow.CollectGvcfCallingMetrics.memory":"3GB",
"PairedEndSingleSampleWorkflow.ConvertToCram.memory":"3GB",
"PairedEndSingleSampleWorkflow.CramToBam.memory":"3GB",
"##_COMMENT9":"RUNTIME SECTION CPU OPTIONS",
"PairedEndSingleSampleWorkflow.CollectQualityYieldMetrics.cpu":1,
"PairedEndSingleSampleWorkflow.CheckFinalVcfExtension.cpu":1,
"PairedEndSingleSampleWorkflow.GetBwaVersion.cpu":1,
"PairedEndSingleSampleWorkflow.SamToFastqAndBwaMemAndMba.cpu":4,
"PairedEndSingleSampleWorkflow.SortSampleBam.cpu":40,
"PairedEndSingleSampleWorkflow.CollectUnsortedReadgroupBamQualityMetrics.cpu":2,
"PairedEndSingleSampleWorkflow.CollectReadgroupBamQualityMetrics.cpu":2,
"PairedEndSingleSampleWorkflow.CollectAggregationMetrics.cpu":2,
"PairedEndSingleSampleWorkflow.CrossCheckFingerprints.cpu":2,
"PairedEndSingleSampleWorkflow.CheckFingerprint.cpu":2,
"PairedEndSingleSampleWorkflow.MarkDuplicates.cpu":2,
"PairedEndSingleSampleWorkflow.CreateSequenceGroupingTSV.cpu":2,
"PairedEndSingleSampleWorkflow.BaseRecalibrator.cpu":2,
"PairedEndSingleSampleWorkflow.GatherBqsrReports.cpu":2,
"PairedEndSingleSampleWorkflow.ApplyBQSR.cpu":2,
"PairedEndSingleSampleWorkflow.GatherBamFiles.cpu":2,
"PairedEndSingleSampleWorkflow.ValidateBamFromCram.cpu":2,
"PairedEndSingleSampleWorkflow.CollectWgsMetrics.cpu":2,
"PairedEndSingleSampleWorkflow.CollectRawWgsMetrics.cpu":2,
"PairedEndSingleSampleWorkflow.CalculateReadGroupChecksum.cpu":2,
"PairedEndSingleSampleWorkflow.CheckContamination.cpu":2,
"PairedEndSingleSampleWorkflow.ScatterIntervalList.cpu":2,
"PairedEndSingleSampleWorkflow.HaplotypeCaller.cpu":2,
"PairedEndSingleSampleWorkflow.MergeVCFs.cpu":2,
"PairedEndSingleSampleWorkflow.ValidateGVCF.cpu":2,
"PairedEndSingleSampleWorkflow.CollectGvcfCallingMetrics.cpu":2,
"PairedEndSingleSampleWorkflow.ConvertToCram.cpu":2,
"PairedEndSingleSampleWorkflow.CramToBam.cpu":2
}