diff --git a/README.md b/README.md index c78c664..977d9fd 100644 --- a/README.md +++ b/README.md @@ -144,11 +144,11 @@ For normal-only or tumour-only samples, exclude the fields for the other state. | `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) | | `gatk_ir_compression` | No | integer | Compression level for BAMs output by IndelRealigner. Default: 0. Range: 0-9 | -| `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_known_indels_vcf_gz` | Yes | path | Absolute path to known indels file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.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_contest_hapmap_3p3_vcf_gz` | Yes | path | Absolute path to HapMap 3.3 biallelic sites file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.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_known_indels_vcf_gz` | Yes | path | Absolute path to known indels file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.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_contest_hapmap_3p3_vcf_gz` | Yes | path | Absolute path to HapMap 3.3 biallelic sites file, e.g., `/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.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. | | `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 b64610a..3c589af 100644 --- a/config/template.config +++ b/config/template.config @@ -41,8 +41,8 @@ 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" // Whether to parallelize the pipeline by chromosome or by splitting into equal-sized intervals // The scatter_count and extra args below only go into effect if parallelize_by_chromosome is disabled @@ -51,10 +51,10 @@ params { split_intervals_extra_args = '' // 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_known_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.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_contest_hapmap_3p3_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.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_known_indels_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.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_contest_hapmap_3p3_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz" // Base resource allocation updater // See README for adding parameters to update the base resource allocations diff --git a/test/configtest-F16.json b/test/configtest-F16.json index 0b2ea0e..e86a9fc 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -52,14 +52,14 @@ "params": { "aligner": "BWA-MEM2-2.2.1", "blcds_registered_dataset": false, - "bundle_contest_hapmap_3p3_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", - "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi", - "bundle_known_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz", - "bundle_known_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi", - "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_mills_and_1000g_gold_standard_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", - "bundle_v0_dbsnp138_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", - "bundle_v0_dbsnp138_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi", + "bundle_contest_hapmap_3p3_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", + "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi", + "bundle_known_indels_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz", + "bundle_known_indels_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi", + "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_mills_and_1000g_gold_standard_indels_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", + "bundle_v0_dbsnp138_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", + "bundle_v0_dbsnp138_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi", "cache_intermediate_pipeline_steps": false, "dataset_id": "A-mini", "docker_container_registry": "ghcr.io/uclahs-cds", @@ -75,7 +75,7 @@ "input": { "BAM": { "tumor": [ - "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" + "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" ] }, "recalibration_table": [ @@ -228,13 +228,13 @@ "memory": "1 GB" } }, - "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", - "reference_fasta_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", - "reference_fasta_fai": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", + "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", + "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", "samples_to_process": [ { "id": "4915723", - "path": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam", + "path": "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam", "sample_type": "tumor" } ], diff --git a/test/configtest-F32.json b/test/configtest-F32.json index 16fd04d..c25b5da 100644 --- a/test/configtest-F32.json +++ b/test/configtest-F32.json @@ -52,14 +52,14 @@ "params": { "aligner": "BWA-MEM2-2.2.1", "blcds_registered_dataset": false, - "bundle_contest_hapmap_3p3_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", - "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi", - "bundle_known_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz", - "bundle_known_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi", - "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_mills_and_1000g_gold_standard_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", - "bundle_v0_dbsnp138_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", - "bundle_v0_dbsnp138_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi", + "bundle_contest_hapmap_3p3_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz", + "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi", + "bundle_known_indels_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz", + "bundle_known_indels_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi", + "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_mills_and_1000g_gold_standard_indels_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", + "bundle_v0_dbsnp138_vcf_gz": "/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", + "bundle_v0_dbsnp138_vcf_gz_tbi": "/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi", "cache_intermediate_pipeline_steps": false, "dataset_id": "A-mini", "docker_container_registry": "ghcr.io/uclahs-cds", @@ -75,7 +75,7 @@ "input": { "BAM": { "tumor": [ - "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" + "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" ] }, "recalibration_table": [ @@ -228,13 +228,13 @@ "memory": "1 GB" } }, - "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", - "reference_fasta_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", - "reference_fasta_fai": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", + "reference_fasta": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta", + "reference_fasta_dict": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", + "reference_fasta_fai": "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", "samples_to_process": [ { "id": "4915723", - "path": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam", + "path": "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam", "sample_type": "tumor" } ], diff --git a/test/nftest.config b/test/nftest.config index e432401..f4bcd8f 100644 --- a/test/nftest.config +++ b/test/nftest.config @@ -39,8 +39,8 @@ 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" // Whether to parallelize the pipeline by chromosome or by splitting into equal-sized intervals // The scatter_count and extra args below only go into effect if parallelize_by_chromosome is disabled @@ -49,10 +49,10 @@ params { split_intervals_extra_args = '' // 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_known_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.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_contest_hapmap_3p3_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.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_known_indels_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.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_contest_hapmap_3p3_vcf_gz = "/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz" } // Setup the pipeline config. DO NOT REMOVE THIS LINE! diff --git a/test/single.yaml b/test/single.yaml index 5507768..8450719 100644 --- a/test/single.yaml +++ b/test/single.yaml @@ -3,4 +3,4 @@ patient_id: TWGSAMIN000001 input: BAM: tumor: - - "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" + - "/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam"