From a08a9f099e7e98f7548a3ff2457555623e2a4edc Mon Sep 17 00:00:00 2001 From: Nick Wiltsie Date: Mon, 28 Oct 2024 16:17:01 -0700 Subject: [PATCH] Update reference paths (#185) --- README.md | 12 ++++++------ config/template.config | 14 +++++++------- test/test-call-gSNP-paired.config | 14 +++++++------- 3 files changed, 20 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index bb002b3..5a3b68c 100644 --- a/README.md +++ b/README.md @@ -120,12 +120,12 @@ For normal-only or tumor-only samples, exclude the fields for the other state. | `cache_intermediate_pipeline_steps` | No | boolean | Set to true to enable process caching from Nextflow; defaults to false | | `scatter_count` | Yes | integer | Number of intervals to divide into for parallelization | | `intervals` | Yes | path | Use all .list in inputs for WGS; Set to absolute path to targeted exome interval file (with .interval_list, .list, .intervals, or .bed suffix) | -| `reference_fasta` | Yes | path | Absolute path to reference genome fasta file, e.g., `/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta` | -| `bundle_mills_and_1000g_gold_standard_indels_vcf_gz` | Yes | path | Absolute path to Mills & 1000G Gold Standard Indels file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz` | -| `bundle_v0_dbsnp138_vcf_gz` | Yes | path | Absolute path to dbsnp file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz` | -| `bundle_hapmap_3p3_vcf_gz` | Yes | path | Absolute path to HapMap 3.3 file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz` | -| `bundle_omni_1000g_2p5_vcf_gz` | Yes | path | Absolute path to 1000 genomes OMNI 2.5 file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz` | -| `bundle_phase1_1000g_snps_high_conf_vcf_gz` | Yes | path | Absolute path to 1000 genomes phase 1 high-confidence file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz` | +| `reference_fasta` | Yes | path | Absolute path to reference genome fasta file, e.g., `/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta` | +| `bundle_mills_and_1000g_gold_standard_indels_vcf_gz` | Yes | path | Absolute path to Mills & 1000G Gold Standard Indels file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz` | +| `bundle_v0_dbsnp138_vcf_gz` | Yes | path | Absolute path to dbsnp file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz` | +| `bundle_hapmap_3p3_vcf_gz` | Yes | path | Absolute path to HapMap 3.3 file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz` | +| `bundle_omni_1000g_2p5_vcf_gz` | Yes | path | Absolute path to 1000 genomes OMNI 2.5 file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz` | +| `bundle_phase1_1000g_snps_high_conf_vcf_gz` | Yes | path | Absolute path to 1000 genomes phase 1 high-confidence file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz` | | `work_dir` | optional | path | Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With ucla_cds, the default is `/scratch` and should only be changed for testing/development. Changing this directory to `/hot` or `/tmp` can lead to high server latency and potential disk space limitations, respectively. | | `docker_container_registry` | optional | string | Registry containing tool Docker images. 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. | diff --git a/config/template.config b/config/template.config index cbb657d..c24d6dc 100644 --- a/config/template.config +++ b/config/template.config @@ -33,15 +33,15 @@ params { // Reference - Used here hg38 decoy version // GATK requires the reference fasta to be accompanied by a .fai index and .dict dictionary associated with the fasta for fast random access - // These can be found in the same folder as the reference here: /hot/ref/reference/GRCh38-BI-20160721 - reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + // These can be found in the same folder as the reference here: /hot/resource/reference-genome/GRCh38-BI-20160721 + reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" // GATK bundle - Used here hg38 decoy version - bundle_mills_and_1000g_gold_standard_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" - bundle_v0_dbsnp138_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz" - bundle_hapmap_3p3_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz" - bundle_omni_1000g_2p5_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz" - bundle_phase1_1000g_snps_high_conf_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz" + 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" // Base resource allocation updater // See README for adding parameters to update the base resource allocations diff --git a/test/test-call-gSNP-paired.config b/test/test-call-gSNP-paired.config index 41ab2b0..d41cfd9 100644 --- a/test/test-call-gSNP-paired.config +++ b/test/test-call-gSNP-paired.config @@ -31,15 +31,15 @@ params { // Reference - Used here hg38 decoy version // GATK requires the reference fasta to be accompanied by a .fai index and .dict dictionary associated with the fasta for fast random access - // These can be found in the same folder as the reference here: /hot/ref/reference/GRCh38-BI-20160721 - reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" + // These can be found in the same folder as the reference here: /hot/resource/reference-genome/GRCh38-BI-20160721 + reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" // GATK bundle - Used here hg38 decoy version - bundle_mills_and_1000g_gold_standard_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" - bundle_v0_dbsnp138_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz" - bundle_hapmap_3p3_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz" - bundle_omni_1000g_2p5_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz" - bundle_phase1_1000g_snps_high_conf_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz" + 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" // Base resource allocation updater // See README for adding parameters to update the base resource allocations