From 000b355c5f76ddd071d0197a8ec0ef3e5d17a60f Mon Sep 17 00:00:00 2001 From: Nicholas Wiltsie Date: Mon, 28 Oct 2024 10:52:40 -0700 Subject: [PATCH] Update reference paths --- README.md | 8 ++++---- config/template.config | 8 ++++---- input/example-test-multi-sample.yaml | 6 +++--- input/example-test-tumor-only.yaml | 2 +- input/example-test.yaml | 4 ++-- test/config/a_mini-all-tools.config | 8 ++++---- test/config/a_mini-muse.config | 8 ++++---- test/config/a_mini-mutect2.config | 8 ++++---- test/config/a_mini-somaticsniper.config | 8 ++++---- test/config/a_mini-strelka2.config | 8 ++++---- test/config/a_mini-two-tools.config | 8 ++++---- test/configtest-F16.json | 20 ++++++++++---------- test/configtest-F32.json | 20 ++++++++++---------- test/yaml/a_mini_n2-std-input.yaml | 4 ++-- test/yaml/a_mini_n2-tumor-only.yaml | 2 +- 15 files changed, 61 insertions(+), 61 deletions(-) diff --git a/README.md b/README.md index 227554ea..a583acff 100644 --- a/README.md +++ b/README.md @@ -194,7 +194,7 @@ input: | `docker_container_registry` | no | string | Registry containing tool Docker images, optional. Default: `ghcr.io/uclahs-cds` | | `base_resource_update` | optional | namespace | Namespace of parameters to update base resource allocations in the pipeline. Usage and structure are detailed in `template.config` and below. | - *Providing `intersect_regions` is required and will limit the final output to just those regions. All regions of the reference genome could be provided as a `bed` file with all contigs, however it is HIGHLY recommended to remove `decoy` contigs from the human reference genome. Including these thousands of small contigs will require the user to increase available memory for `Mutect2` and will cause a very long runtime for `Strelka2`. See [Discussion here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/216). For `uclahs-cds` users, a GRCh38 `bed.gz` file can be found here: `/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz`. + *Providing `intersect_regions` is required and will limit the final output to just those regions. All regions of the reference genome could be provided as a `bed` file with all contigs, however it is HIGHLY recommended to remove `decoy` contigs from the human reference genome. Including these thousands of small contigs will require the user to increase available memory for `Mutect2` and will cause a very long runtime for `Strelka2`. See [Discussion here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/216). For `uclahs-cds` users, a GRCh38 `bed.gz` file can be found here: `/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz`. ### Base resource allocation updaters To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the [input.config](config/template.config) file. The default allocations can be found in the [node-specific config files](./config/) @@ -258,8 +258,8 @@ base_resource_update { | filter_mutect_calls_extra_args | no | string | Additional arguments for the FilterMutectCalls command | | gatk_command_mem_diff | yes | nextflow.util.MemoryUnit | How much to subtract from the task's allocated memory where the remainder is the Java heap max. (should not be changed unless task fails for memory related reasons) | | scatter_count | yes | int | Number of intervals to split the desired interval into. Mutect2 will call each interval seperately. | -| germline_resource_gnomad_vcf | no | path | A stripped down version of the [gnomAD VCF](https://gnomad.broadinstitute.org/) stripped of all unneeded INFO fields, keeping only AF, currently available for GRCh38:`/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz` and GRCh37: `/hot/ref/tool-specific-input/GATK/GRCh37/af-only-gnomad.raw.sites.vcf`. | -| panel_of_normals_vcf | no | path | VCF file of sites observed in normal. Currently available for GRCh38: `/hot/ref/tool-specific-input/GATK/GRCh38/1000g_pon.hg38.vcf.gz`. This could be useful for tumor only mode. | +| germline_resource_gnomad_vcf | no | path | A stripped down version of the [gnomAD VCF](https://gnomad.broadinstitute.org/) stripped of all unneeded INFO fields, keeping only AF, currently available for GRCh38:`/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz` and GRCh37: `/hot/resource/tool-specific-input/GATK/GRCh37/af-only-gnomad.raw.sites.vcf`. | +| panel_of_normals_vcf | no | path | VCF file of sites observed in normal. Currently available for GRCh38: `/hot/resource/tool-specific-input/GATK/GRCh38/1000g_pon.hg38.vcf.gz`. This could be useful for tumor only mode. | #### MuSE Specific Configuration | Input | Required | Type | Description | @@ -348,7 +348,7 @@ Tumor BAM: `/hot/resource/pipeline_testing_set/WGS/GRCh38/A/full/CPCG0000000196- |call_sIndel_Manta |1h 35m 25s |1848.6% |11.7 GB | |call_sSNV_Strelka2 |59m 19s |3234.0% |8.2 GB | -Therefore, we strongly suggest to use the `--callRegions` if the non-canonical region is unnecessary. `-callRegions`'s input `bed.gz` file can be found here: `/hot/ref/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz`. For other genome version, you can use [UCSC Liftover](https://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert. +Therefore, we strongly suggest to use the `--callRegions` if the non-canonical region is unnecessary. `-callRegions`'s input `bed.gz` file can be found here: `/hot/resource/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz`. For other genome version, you can use [UCSC Liftover](https://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert. #### MuSE v2.0 MuSE v2.0 was tested with a normal/tumor paired CPCG0196 WGS sample on a F32 slurm-dev node. diff --git a/config/template.config b/config/template.config index cda6978f..a2af5f08 100644 --- a/config/template.config +++ b/config/template.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = [] // 'somaticsniper', 'strelka2', 'mutect2', 'muse' - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' output_dir = '' dataset_id = '' // set params.exome to TRUE will add the '--exome' option when running Manta and Strelka2 @@ -31,10 +31,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Variant Intersection options ncbi_build = 'GRCh38' diff --git a/input/example-test-multi-sample.yaml b/input/example-test-multi-sample.yaml index 0e4b2aba..8c26c0b6 100644 --- a/input/example-test-multi-sample.yaml +++ b/input/example-test-multi-sample.yaml @@ -3,9 +3,9 @@ patient_id: 'TWGSAMIN000001' # For multi samples, list the BAMs under the corresponding state (normal or tumor). input: normal: - - BAM: /hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam + - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam tumor: - - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam + - BAM: /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 - - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam + - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n1_getpileupsummaries_calculatecontamination.table diff --git a/input/example-test-tumor-only.yaml b/input/example-test-tumor-only.yaml index 9cb44767..67585141 100644 --- a/input/example-test-tumor-only.yaml +++ b/input/example-test-tumor-only.yaml @@ -2,5 +2,5 @@ patient_id: 'TWGSAMIN000001' input: tumor: - - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam + - BAM: /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-n1_getpileupsummaries_calculatecontamination.table diff --git a/input/example-test.yaml b/input/example-test.yaml index ee0333ec..7dfbb617 100644 --- a/input/example-test.yaml +++ b/input/example-test.yaml @@ -3,7 +3,7 @@ patient_id: 'TWGSAMIN000001' # For multi samples, just list all the bams under the normal or tumor. input: normal: - - BAM: /hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam + - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam tumor: - - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam + - BAM: /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-n1_getpileupsummaries_calculatecontamination.table diff --git a/test/config/a_mini-all-tools.config b/test/config/a_mini-all-tools.config index 72b48ef4..9a8e8a63 100644 --- a/test/config/a_mini-all-tools.config +++ b/test/config/a_mini-all-tools.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = ['somaticsniper', 'strelka2', 'mutect2', 'muse'] - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' dataset_id = 'TWGSAMIN' // setting params.exome to TRUE will add the '--exome' option when running manta and strelka2 and the -E option when running MuSE exome = false @@ -29,10 +29,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Intersect options ncbi_build = 'GRCh38' diff --git a/test/config/a_mini-muse.config b/test/config/a_mini-muse.config index 4a456d04..d8f6fa4f 100644 --- a/test/config/a_mini-muse.config +++ b/test/config/a_mini-muse.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = ['muse'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse' - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' dataset_id = 'TWGSAMIN' // set params.exome to TRUE will add the '--exome' option when running manta and strelka2 // set params.exome to TRUE will add the '-E' option when running MuSE @@ -30,10 +30,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Intersect options ncbi_build = 'GRCh38' diff --git a/test/config/a_mini-mutect2.config b/test/config/a_mini-mutect2.config index 5d89031a..ff4b3ea8 100644 --- a/test/config/a_mini-mutect2.config +++ b/test/config/a_mini-mutect2.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = ['mutect2'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse' - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' dataset_id = 'TWGSAMIN' // set params.exome to TRUE will add the '--exome' option when running manta and strelka2 // set params.exome to TRUE will add the '-E' option when running MuSE @@ -30,10 +30,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Intersect options ncbi_build = 'GRCh38' diff --git a/test/config/a_mini-somaticsniper.config b/test/config/a_mini-somaticsniper.config index f3d64fc8..9c0b75cf 100644 --- a/test/config/a_mini-somaticsniper.config +++ b/test/config/a_mini-somaticsniper.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = ['somaticsniper'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse' - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' dataset_id = 'TWGSAMIN' // set params.exome to TRUE will add the '--exome' option when running manta and strelka2 // set params.exome to TRUE will add the '-E' option when running MuSE @@ -30,10 +30,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Intersect options ncbi_build = 'GRCh38' diff --git a/test/config/a_mini-strelka2.config b/test/config/a_mini-strelka2.config index 2d0ef50a..40b06154 100644 --- a/test/config/a_mini-strelka2.config +++ b/test/config/a_mini-strelka2.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = ['strelka2'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse' - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' dataset_id = 'TWGSAMIN' // set params.exome to TRUE will add the '--exome' option when running manta and strelka2 // set params.exome to TRUE will add the '-E' option when running MuSE @@ -30,10 +30,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Intersect options ncbi_build = 'GRCh38' diff --git a/test/config/a_mini-two-tools.config b/test/config/a_mini-two-tools.config index 1052e258..9ee7c01c 100644 --- a/test/config/a_mini-two-tools.config +++ b/test/config/a_mini-two-tools.config @@ -12,8 +12,8 @@ includeConfig "${projectDir}/config/methods.config" params { algorithm = ['somaticsniper', 'strelka2'] - reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' - intersect_regions = '/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' + reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta' + intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz' dataset_id = 'TWGSAMIN' // setting params.exome to TRUE will add the '--exome' option when running manta and strelka2 and the -E option when running MuSE exome = false @@ -29,10 +29,10 @@ params { filter_mutect_calls_extra_args = '' gatk_command_mem_diff = 500.MB scatter_count = 50 - germline_resource_gnomad_vcf = '/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' + germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz' // MuSE options - dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' + dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz' // Intersect options ncbi_build = 'GRCh38' diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 81d8b4ea..50aea11b 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -69,7 +69,7 @@ "cache_intermediate_pipeline_steps": false, "call_ssnv_r_version": "dev", "dataset_id": "TWGSAMIN", - "dbSNP": "/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz", + "dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz", "docker_container_registry": "ghcr.io/uclahs-cds", "docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.17", "docker_image_GATK": "broadinstitute/gatk:4.5.0.0", @@ -88,24 +88,24 @@ "filter_mutect_calls_extra_args": "", "gatk_command_mem_diff": "500 MB", "germline": true, - "germline_resource_gnomad_vcf": "/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz", - "germline_resource_gnomad_vcf_index": "/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi", + "germline_resource_gnomad_vcf": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz", + "germline_resource_gnomad_vcf_index": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi", "input": { "normal": [ { - "BAM": "/hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam" + "BAM": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam" } ], "tumor": [ { - "BAM": "/hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam", + "BAM": "/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" } ] }, "input_type": "bam", - "intersect_regions": "/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz", - "intersect_regions_index": "/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi", + "intersect_regions": "/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz", + "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", "keep_input_prefix": false, "log_output_dir": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z", "manta_version": "1.6.0", @@ -241,17 +241,17 @@ "memory": "1 GB" } }, - "reference": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", "sample_id": "0192847", "samples_to_process": [ { "contamination_table": "null", "id": "0192847", "orig_id": "0192847", - "path": "/hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam", + "path": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam", "sample_type": "normal" }, - "{orig_id=0192847, id=0192847, path=/hot/resource/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}" + "{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}" ], "save_intermediate_files": false, "scatter_count": "50", diff --git a/test/configtest-F32.json b/test/configtest-F32.json index ffbd285b..8288c1f9 100644 --- a/test/configtest-F32.json +++ b/test/configtest-F32.json @@ -69,7 +69,7 @@ "cache_intermediate_pipeline_steps": false, "call_ssnv_r_version": "dev", "dataset_id": "TWGSAMIN", - "dbSNP": "/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz", + "dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz", "docker_container_registry": "ghcr.io/uclahs-cds", "docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.17", "docker_image_GATK": "broadinstitute/gatk:4.5.0.0", @@ -88,24 +88,24 @@ "filter_mutect_calls_extra_args": "", "gatk_command_mem_diff": "500 MB", "germline": true, - "germline_resource_gnomad_vcf": "/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz", - "germline_resource_gnomad_vcf_index": "/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi", + "germline_resource_gnomad_vcf": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz", + "germline_resource_gnomad_vcf_index": "/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi", "input": { "normal": [ { - "BAM": "/hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam" + "BAM": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam" } ], "tumor": [ { - "BAM": "/hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam", + "BAM": "/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" } ] }, "input_type": "bam", - "intersect_regions": "/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz", - "intersect_regions_index": "/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi", + "intersect_regions": "/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz", + "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", "keep_input_prefix": false, "log_output_dir": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847/log-call-sSNV-VER.SI.ON-19970704T165655Z", "manta_version": "1.6.0", @@ -239,17 +239,17 @@ "memory": "1 GB" } }, - "reference": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", "sample_id": "0192847", "samples_to_process": [ { "contamination_table": "null", "id": "0192847", "orig_id": "0192847", - "path": "/hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam", + "path": "/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam", "sample_type": "normal" }, - "{orig_id=0192847, id=0192847, path=/hot/resource/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}" + "{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}" ], "save_intermediate_files": false, "scatter_count": "50", diff --git a/test/yaml/a_mini_n2-std-input.yaml b/test/yaml/a_mini_n2-std-input.yaml index 9d1ee3fb..b47e134b 100644 --- a/test/yaml/a_mini_n2-std-input.yaml +++ b/test/yaml/a_mini_n2-std-input.yaml @@ -2,7 +2,7 @@ patient_id: 'TWGSAMIN000001' input: normal: - - BAM: /hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam + - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam tumor: - - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam + - BAM: /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 diff --git a/test/yaml/a_mini_n2-tumor-only.yaml b/test/yaml/a_mini_n2-tumor-only.yaml index 702fa68f..785f9df6 100644 --- a/test/yaml/a_mini_n2-tumor-only.yaml +++ b/test/yaml/a_mini_n2-tumor-only.yaml @@ -2,5 +2,5 @@ patient_id: 'TWGSAMIN000001' input: tumor: - - BAM: /hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam + - BAM: /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