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Update reference paths (#185)
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@nwiltsie
nwiltsie authored Oct 28, 2024
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -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. |
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14 changes: 7 additions & 7 deletions config/template.config
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Expand Up @@ -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
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14 changes: 7 additions & 7 deletions test/test-call-gSNP-paired.config
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Expand Up @@ -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
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