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nwiltsienwiltsie
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Update configtest expected results
1 parent 633c749 commit da7639b

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Lines changed: 42 additions & 68 deletions

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‎test/configtest-F16.json‎

Lines changed: 14 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -55,10 +55,7 @@
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"GATK_version": "4.6.1.0",
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"MuSE_version": "2.1.2",
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"algorithm": [
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"somaticsniper",
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"strelka2",
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"mutect2",
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"muse"
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"somaticsniper"
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],
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"bam_readcount_version": "1.0.1",
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"base_allocations": {
@@ -119,8 +116,8 @@
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"bpg_version": "7.1.0",
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"cache_intermediate_pipeline_steps": false,
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"call_ssnv_r_version": "dev",
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"dataset_id": "TWGSAMIN",
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"dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz",
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"dataset_id": "dataset_004",
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"dbSNP": "/example/dbSNP-155/GCF_000001405.39.gz",
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"docker_container_registry": "ghcr.io/uclahs-cds",
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"docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.21",
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"docker_image_GATK": "broadinstitute/gatk:4.6.1.0",
@@ -139,24 +136,24 @@
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"filter_mutect_calls_extra_args": "",
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"gatk_command_mem_diff": "500 MB",
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"germline": true,
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"germline_resource_gnomad_vcf": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz",
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"germline_resource_gnomad_vcf_index": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi",
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"germline_resource_gnomad_vcf": "/example/genomics-public-data/resources/broad/hg38/v0/af-only-gnomad.hg38.vcf.gz",
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"germline_resource_gnomad_vcf_index": "/example/genomics-public-data/resources/broad/hg38/v0/af-only-gnomad.hg38.vcf.gz.tbi",
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"input": {
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"normal": [
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{
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"BAM": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam"
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"BAM": "/path/to/normal.bam"
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}
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],
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"tumor": [
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{
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"BAM": "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam",
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"contamination_table": "/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table"
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"BAM": "/path/to/tumor.bam",
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"contamination_table": "/path/to/contamination.table"
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}
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]
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},
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"input_type": "bam",
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"intersect_regions": "/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz",
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"intersect_regions_index": "/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi",
155+
"intersect_regions": "/example/genome/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz",
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"intersect_regions_index": "/example/genome/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi",
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"keep_input_prefix": false,
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"log_output_dir": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z",
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"manta_version": "1.6.0",
@@ -172,9 +169,9 @@
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"output_dir": "/tmp/outputs",
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"output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847",
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"panel_of_normals_vcf": "",
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"patient_id": "TWGSAMIN000001",
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"patient_id": "patient_id",
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"pipeval_version": "5.1.0",
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"reference": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
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"reference": "/example/genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
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"retry_information": {
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"call_sIndel_Manta": {
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"memory": {
@@ -255,10 +252,10 @@
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"contamination_table": "null",
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"id": "0192847",
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"orig_id": "0192847",
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"path": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam",
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"path": "/path/to/normal.bam",
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"sample_type": "normal"
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},
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"{orig_id=0192847, id=0192847, path=/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam, contamination_table=/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table, sample_type=tumor}"
258+
"{orig_id=0192847, id=0192847, path=/path/to/tumor.bam, contamination_table=/path/to/contamination.table, sample_type=tumor}"
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],
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"save_intermediate_files": false,
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"scatter_count": "50",

‎test/configtest-F32.json‎

Lines changed: 28 additions & 51 deletions
Original file line numberDiff line numberDiff line change
@@ -55,10 +55,7 @@
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"GATK_version": "4.6.1.0",
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"MuSE_version": "2.1.2",
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"algorithm": [
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"somaticsniper",
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"strelka2",
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"mutect2",
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"muse"
58+
"somaticsniper"
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],
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"bam_readcount_version": "1.0.1",
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"base_allocations": {
@@ -119,8 +116,8 @@
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"bpg_version": "7.1.0",
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"cache_intermediate_pipeline_steps": false,
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"call_ssnv_r_version": "dev",
122-
"dataset_id": "TWGSAMIN",
123-
"dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz",
119+
"dataset_id": "dataset_004",
120+
"dbSNP": "/example/dbSNP-155/GCF_000001405.39.gz",
124121
"docker_container_registry": "ghcr.io/uclahs-cds",
125122
"docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.21",
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"docker_image_GATK": "broadinstitute/gatk:4.6.1.0",
@@ -138,27 +135,20 @@
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"exome": false,
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"filter_mutect_calls_extra_args": "",
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"gatk_command_mem_diff": "500 MB",
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"germline": true,
142-
"germline_resource_gnomad_vcf": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz",
143-
"germline_resource_gnomad_vcf_index": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi",
138+
"germline_resource_gnomad_vcf": "/example/genomics-public-data/resources/broad/hg38/v0/af-only-gnomad.hg38.vcf.gz",
144139
"input": {
145-
"normal": [
146-
{
147-
"BAM": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam"
148-
}
149-
],
150-
"tumor": [
151-
{
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"BAM": "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam",
153-
"contamination_table": "/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table"
154-
}
155-
]
140+
"muse": "/path/to/muse.vcf.gz",
141+
"mutect2": "/path/to/mutect2.vcf.gz",
142+
"somaticsniper": "/path/to/somaticsniper.vcf.gz",
143+
"strelka2": "/path/to/strelka2.vcf.gz"
156144
},
157-
"input_type": "bam",
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"intersect_regions": "/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz",
159-
"intersect_regions_index": "/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi",
145+
"input_normal_id": "normal_id",
146+
"input_tumor_id": "tumor_id",
147+
"input_type": "vcf",
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"intersect_regions": "/example/genome/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz",
149+
"intersect_regions_index": "/example/genome/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi",
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"keep_input_prefix": false,
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"log_output_dir": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z",
151+
"log_output_dir": "/tmp/outputs/call-sSNV-VER.SI.ON/tumor-id/log-call-sSNV-VER.SI.ON-19970704T165655Z",
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"manta_version": "1.6.0",
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"max_cpus": "32",
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"max_memory": "64 GB",
@@ -168,13 +158,12 @@
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"min_time": "1s",
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"mutect2_extra_args": "",
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"ncbi_build": "GRCh38",
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"normal_id": "0192847",
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"normal_id": "normal-id",
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"output_dir": "/tmp/outputs",
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"output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847",
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"panel_of_normals_vcf": "",
175-
"patient_id": "TWGSAMIN000001",
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"output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/tumor-id",
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"patient_id": "patient_id",
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"pipeval_version": "5.1.0",
177-
"reference": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
166+
"reference": "/example/genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
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"retry_information": {
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"call_sIndel_Manta": {
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"memory": {
@@ -249,26 +238,24 @@
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}
250239
}
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},
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"sample_id": "0192847",
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"sample_id": "tumor-id",
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"samples_to_process": [
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{
255-
"contamination_table": "null",
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"id": "0192847",
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"orig_id": "0192847",
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"path": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam",
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"sample_type": "normal"
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"algorithm": "muse",
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"path": "/path/to/muse.vcf.gz"
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},
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"{orig_id=0192847, id=0192847, path=/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam, contamination_table=/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table, sample_type=tumor}"
247+
"{path=/path/to/mutect2.vcf.gz, algorithm=mutect2}",
248+
"{path=/path/to/somaticsniper.vcf.gz, algorithm=somaticsniper}",
249+
"{path=/path/to/strelka2.vcf.gz, algorithm=strelka2}"
262250
],
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"save_intermediate_files": false,
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"scatter_count": "50",
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"single_NT_paired": true,
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"somaticsniper_version": "1.0.5.0",
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"split_intervals_extra_args": "",
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"src_util_version": "1.2.0",
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"strelka2_version": "2.9.10",
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"tabix_extra_args": "",
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"tumor_id": "0192847",
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"tumor_id": "tumor-id",
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"ubuntu_version": "20.04",
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"ucla_cds": true,
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"use_intersect_regions": true,
@@ -402,9 +389,6 @@
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},
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"withName:call_sSNV_Strelka2": {
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"cpus": "8",
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"ext": {
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"retry_codes": []
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},
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"memory": {
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"1": "2 GB",
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"2": "14 GB",
@@ -482,29 +466,22 @@
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},
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"report": {
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"enabled": true,
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"file": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
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"file": "/tmp/outputs/call-sSNV-VER.SI.ON/tumor-id/log-call-sSNV-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
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},
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"resource_handler": {
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"handle_resources": "closure()",
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"set_resource_limit_params": "closure()",
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"set_retry": "closure()",
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"setup_retry": "closure()"
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},
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"sm_tag": "0192847",
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"timeline": {
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"enabled": true,
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"file": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"
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"file": "/tmp/outputs/call-sSNV-VER.SI.ON/tumor-id/log-call-sSNV-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"
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},
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"trace": {
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"enabled": true,
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"file": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z/nextflow-log/trace.txt"
483+
"file": "/tmp/outputs/call-sSNV-VER.SI.ON/tumor-id/log-call-sSNV-VER.SI.ON-19970704T165655Z/nextflow-log/trace.txt"
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},
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"valid_algorithms": [
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"somaticsniper",
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"strelka2",
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"mutect2",
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"muse"
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],
508485
"workDir": "/scratch/8543"
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}
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}

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