From 718ae585465593d4df74b9a95e6d47bc56a7d8ab Mon Sep 17 00:00:00 2001 From: Mark Schreiber Date: Tue, 9 Nov 2021 15:20:11 -0500 Subject: [PATCH] docs: miniwdl engine docs and example project for GATK best practices (#158) * add engine docs * add miniwdl examples --- .../README.md | 6 + .../agc-project.yaml | 72 + .../MANIFEST.json | 7 + .../gatk4-basic-joint-genotyping.inputs.json | 12 + .../gatk4-basic-joint-genotyping.wdl | 329 + .../gatk4-data-processing/MANIFEST.json | 7 + ...riant-discovery-gatk4.hg38.wgs.inputs.json | 29 + ...processing-for-variant-discovery-gatk4.wdl | 719 + .../gatk4-germline-snps-indels/MANIFEST.json | 7 + ...typecaller-gvcf-gatk4.hg38.wgs.inputs.json | 10 + .../haplotypecaller-gvcf-gatk4.wdl | 264 + .../MANIFEST.json | 5 + ...k4-rnaseq-germline-snps-indels.inputs.json | 20 + .../gatk4-rnaseq-germline-snps-indels.wdl | 800 ++ .../bam-to-unmapped-bams/MANIFEST.json | 7 + .../bam-to-unmapped-bams.inputs.json | 3 + .../bam-to-unmapped-bams.wdl | 129 + .../cram-to-bam/MANIFEST.json | 7 + .../cram-to-bam/cram-to-bam.inputs.json | 8 + .../cram-to-bam/cram-to-bam.wdl | 144 + .../MANIFEST.json | 7 + ...erleaved-fastq-to-paired-fastq.inputs.json | 3 + .../interleaved-fastq-to-paired-fastq.wdl | 54 + .../MANIFEST.json | 7 + .../paired-fastq-to-unmapped-bam.wdl | 158 + .../paired-fastq-to-unmapped-inputs.json | 13 + .../seq-format-validation/MANIFEST.json | 7 + .../seq-format-validation/validate-bam.wdl | 90 + .../validate-bams.input.json | 6 + packages/cdk/package-lock.json | 11385 +++++++++++++++- .../en/docs/Workflow engines/cromwell.md | 1 + .../en/docs/Workflow engines/miniwdl.md | 75 + .../en/docs/Workflow engines/nextflow.md | 3 +- site/package-lock.json | 1330 +- site/themes/docsy | 2 +- 35 files changed, 15678 insertions(+), 48 deletions(-) create mode 100644 examples/gatk-best-practices-project-miniwdl/README.md create mode 100644 examples/gatk-best-practices-project-miniwdl/agc-project.yaml create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-bam.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-inputs.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-validation/MANIFEST.json create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bam.wdl create mode 100644 examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bams.input.json create mode 100644 site/content/en/docs/Workflow engines/miniwdl.md diff --git a/examples/gatk-best-practices-project-miniwdl/README.md b/examples/gatk-best-practices-project-miniwdl/README.md new file mode 100644 index 00000000..03e2f630 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/README.md @@ -0,0 +1,6 @@ +## Introduction + +This project includes workflows based on [GATK Best Practices](https://gatk.broadinstitute.org/hc/en-us), developed by +the [Broad Institute](https://www.broadinstitute.org/). More information on how these workflows work is available in +the [GATK Workflows Github repository](/~https://github.com/gatk-workflows). + diff --git a/examples/gatk-best-practices-project-miniwdl/agc-project.yaml b/examples/gatk-best-practices-project-miniwdl/agc-project.yaml new file mode 100644 index 00000000..8396b352 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/agc-project.yaml @@ -0,0 +1,72 @@ +--- +name: GATK +schemaVersion: 1 +workflows: + gatk4-data-processing: + type: + language: wdl + version: 1.0 + sourceURL: ./gatk4-data-processing + gatk4-germline-snps-indels: + type: + language: wdl + version: 1.0 + sourceURL: ./gatk4-germline-snps-indels + gatk4-basic-joint-genotyping: + type: + language: wdl + version: 1.0 + sourceURL: ./gatk4-basic-joint-genotyping + seq-format-validation: + type: + language: wdl + version: 1.0 + sourceURL: ./seq-format-validation + bam-to-unmapped-bams: + type: + language: wdl + version: 1.0 + sourceURL: ./seq-format-conversions/bam-to-unmapped-bams + cram-to-bam: + type: + language: wdl + version: 1.0 + sourceURL: ./seq-format-conversions/cram-to-bam + interleaved-fastq-to-paired-fastq: + type: + language: wdl + version: 1.0 + sourceURL: ./seq-format-conversions/interleaved-fastq-to-paired-fastq + paired-fastq-to-unmapped-bam: + type: + language: wdl + version: 1.0 + sourceURL: ./seq-format-conversions/paired-fastq-to-unmapped-bam + gatk4-rnaseq-germline-snps-indels: + type: + language: wdl + version: 1.0 + sourceURL: ./gatk4-rnaseq-germline-snps-indels +data: + - location: s3://gatk-test-data + readOnly: true + - location: s3://broad-references + readOnly: true + - location: s3://1000genomes-dragen-3.7.6 + readOnly: true + - location: s3://healthai-public-assets-us-east-1/agc-demo-data + readOnly: true +contexts: + # The on demand context uses on-demand EC2 instances which may be more expensive but will not be interrupted + onDemandCtx: + requestSpotInstances: false + engines: + - type: wdl + engine: miniwdl + + # The spot context uses EC2 spot instances which are usually cheaper but may be interrupted + spotCtx: + requestSpotInstances: true + engines: + - type: wdl + engine: miniwdl diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/MANIFEST.json new file mode 100644 index 00000000..5f3d8ab8 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "gatk4-basic-joint-genotyping.wdl", + "inputFileURLs": [ + "gatk4-basic-joint-genotyping.inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.inputs.json b/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.inputs.json new file mode 100644 index 00000000..0a370b92 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.inputs.json @@ -0,0 +1,12 @@ +{ + "BasicJointGenotyping.input_gvcfs": [ + "s3://1000genomes-dragen-3.7.6/data/individuals/hg38-graph-based/NA12329/NA12329.hard-filtered.gvcf.gz", + "s3://1000genomes-dragen-3.7.6/data/individuals/hg38-graph-based/NA06984/NA06984.hard-filtered.gvcf.gz", + "s3://1000genomes-dragen-3.7.6/data/individuals/hg38-graph-based/NA06989/NA06989.hard-filtered.gvcf.gz" + ], + "BasicJointGenotyping.ref_fasta": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", + "BasicJointGenotyping.ref_fasta_index": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", + "BasicJointGenotyping.ref_dict": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dict", + "BasicJointGenotyping.interval_list": "s3://broad-references/hg38/v0/hg38.even.handcurated.20k.chr20_test.intervals", + "BasicJointGenotyping.callset_name": "Trio" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.wdl b/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.wdl new file mode 100644 index 00000000..607b75f0 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.wdl @@ -0,0 +1,329 @@ +version 1.0 + +## Copyright Broad Institute, 2020 +## +## This WDL implements a basic joint discovery workflow with GATK4. It is based +## on the Best Practices pipeline published by the GATK team here: +## /~https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/JointGenotyping.wdl +## However this workflow is not vetted for production work and is only intended +## for testing, demonstration and teaching purposes. +## +## Requirements/expectations : +## - One or more GVCFs produced by HaplotypeCaller in GVCF mode +## +## Outputs : +## - A VCF file and its index, containing variants joint-called from the input samples, +## without any filtering applied after calling. +## +## Cromwell version support +## - Successfully tested with 53.1 +## +## Runtime parameters may be optimized for Broad's Google Cloud Platform implementation. +## For program versions, see docker containers. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/openwdl/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. See the respective containers +## for relevant information. + +# WORKFLOW DEFINITION + +# Basic Joint Genotyping with GATK4 (not Best Practices, just demo) +workflow BasicJointGenotyping { + + input { + Array[File] input_gvcfs + File interval_list + String callset_name + + File ref_fasta + File ref_fasta_index + File ref_dict + + String gatk_path = "/gatk/gatk" + String gatk_docker = "broadinstitute/gatk:4.1.8.1" + } + + scatter (input_gvcf in input_gvcfs) { + + call RenameAndIndexFile { + input: + input_file = input_gvcf, + expected_suffix = ".g.vcf.gz", + index_suffix = ".tbi", + gatk_path = gatk_path, + docker = gatk_docker + } + } + + Array[String] calling_intervals = read_lines(interval_list) + + scatter (interval in calling_intervals) { + + call ImportGVCFs { + input: + input_gvcfs = RenameAndIndexFile.renamed_input, + input_gvcf_indices = RenameAndIndexFile.output_index, + workspace_dir_name = "genomicsdb", + interval = interval, + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + ref_dict = ref_dict, + gatk_path = gatk_path, + docker = gatk_docker + } + + call GenotypeGVCFs { + input: + workspace_tar = ImportGVCFs.output_workspace, + interval = interval, + output_vcf_filename = callset_name + "_scatter.vcf.gz", + output_index_suffix = ".tbi", + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + ref_dict = ref_dict, + gatk_path = gatk_path, + docker = gatk_docker + } + } + + call MergeVCFs { + input: + input_vcfs = GenotypeGVCFs.output_vcf, + input_vcf_indices = GenotypeGVCFs.output_vcf_index, + merged_vcf_filename = callset_name + ".vcf.gz", + output_index_suffix = ".tbi", + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + ref_dict = ref_dict, + gatk_path = gatk_path, + docker = gatk_docker + } + + output { + File merged_vcf = MergeVCFs.output_vcf + File merged_vcf_index = MergeVCFs.output_vcf_index + } +} + +# TASK DEFINITIONS + +task RenameAndIndexFile { + + input { + File input_file + String expected_suffix + String index_suffix + + # Environment parameters + String gatk_path + String docker + + # Resourcing parameters + String? java_opt + Int? mem_gb + Int? retry_attempts + } + + Int machine_mem_gb = select_first([mem_gb, 7]) + Int command_mem_gb = machine_mem_gb - 1 + + # Does the input file have the correct suffix? + Boolean good_suffix = sub(basename(input_file), ".*\\.", "") == expected_suffix + + String new_name = if good_suffix then basename(input_file) else basename(input_file) + expected_suffix + String index_name = new_name + index_suffix + + command { + set -euo pipefail + + cp ~{input_file} ~{new_name} + + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}G ~{java_opt}" \ + IndexFeatureFile \ + -I ~{new_name} \ + -O ~{index_name} + } + + runtime { + docker: docker + memory: machine_mem_gb + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + + output { + File renamed_input = "~{new_name}" + File output_index = "~{index_name}" + } + +} + +task ImportGVCFs { + + input { + Array[File] input_gvcfs + Array[File] input_gvcf_indices + String interval + String workspace_dir_name + + File ref_fasta + File ref_fasta_index + File ref_dict + + # Environment parameters + String gatk_path + String docker + + # Resourcing parameters + String? java_opt + Int? mem_gb + Int? retry_attempts + } + + parameter_meta { + input_gvcfs: { + description: "an GVCF file used as input", + localization_optional: true + } + input_gvcf_indices: { + description: "an index file for a GVCF file used as input", + localization_optional: true + } + } + + Int machine_mem_gb = select_first([mem_gb, 15]) + Int command_mem_gb = machine_mem_gb - 3 + + String tarred_workspace_name = workspace_dir_name + ".tar" + + command <<< + set -euo pipefail + + rm -rf ~{workspace_dir_name} + + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}G ~{java_opt}" \ + GenomicsDBImport \ + -V ~{sep=' -V ' input_gvcfs} \ + -L ~{interval} \ + --genomicsdb-workspace-path ~{workspace_dir_name} \ + --batch-size 50 \ + --reader-threads 5 \ + --merge-input-intervals \ + --consolidate + + tar -cf ~{tarred_workspace_name} ~{workspace_dir_name} + >>> + + runtime { + docker: docker + memory: machine_mem_gb + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + + output { + File output_workspace = "~{tarred_workspace_name}" + } +} + +task GenotypeGVCFs { + + input { + File workspace_tar + String interval + + String output_vcf_filename + String output_index_suffix + + File ref_fasta + File ref_fasta_index + File ref_dict + + # Environment parameters + String gatk_path + String docker + + # Resourcing parameters + String? java_opt + Int? mem_gb + Int? retry_attempts + } + + Int machine_mem_gb = select_first([mem_gb, 7]) + Int command_mem_gb = machine_mem_gb - 1 + + command <<< + set -euo pipefail + + tar -xf ~{workspace_tar} + WORKSPACE=$(basename ~{workspace_tar} .tar) + + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}G ~{java_opt}" \ + GenotypeGVCFs \ + -R ~{ref_fasta} \ + -V gendb://$WORKSPACE \ + -L ~{interval} \ + -O ~{output_vcf_filename} \ + -G StandardAnnotation -G AS_StandardAnnotation \ + --allow-old-rms-mapping-quality-annotation-data \ + --merge-input-intervals + >>> + + runtime { + docker: docker + memory: machine_mem_gb + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + + output { + File output_vcf = "~{output_vcf_filename}" + File output_vcf_index = "~{output_vcf_filename + output_index_suffix}" + } +} + +task MergeVCFs { + + input { + Array[File] input_vcfs + Array[File] input_vcf_indices + + String merged_vcf_filename + String output_index_suffix + + File ref_fasta + File ref_fasta_index + File ref_dict + + # Environment parameters + String gatk_path + String docker + + # Resourcing parameters + String? java_opt + Int? mem_gb + Int? retry_attempts + } + + Int machine_mem_gb = select_first([mem_gb, 7]) + Int command_mem_gb = machine_mem_gb - 1 + + command { + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}G ~{java_opt}" \ + MergeVcfs \ + -I ~{sep=' -I ' input_vcfs} \ + -O ~{merged_vcf_filename} + } + + runtime { + docker: docker + memory: machine_mem_gb + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + + output { + File output_vcf = "~{merged_vcf_filename}" + File output_vcf_index = "~{merged_vcf_filename + output_index_suffix}" + } + +} diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/MANIFEST.json new file mode 100644 index 00000000..4fdb84f4 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "processing-for-variant-discovery-gatk4.wdl", + "inputFileURLs": [ + "processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json b/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json new file mode 100644 index 00000000..8376a28a --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json @@ -0,0 +1,29 @@ +{ + "PreProcessingForVariantDiscovery_GATK4.sample_name": "NA12878", + "PreProcessingForVariantDiscovery_GATK4.ref_name": "hg38", + "PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "s3://gatk-test-data/wgs_ubam/NA12878_24RG/NA12878_24RG_small.txt", + "PreProcessingForVariantDiscovery_GATK4.unmapped_bam_suffix": ".bam", + + "PreProcessingForVariantDiscovery_GATK4.ref_dict": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dict", + "PreProcessingForVariantDiscovery_GATK4.ref_fasta": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", + "PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", + "PreProcessingForVariantDiscovery_GATK4.ref_alt": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt", + "PreProcessingForVariantDiscovery_GATK4.ref_sa": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa", + "PreProcessingForVariantDiscovery_GATK4.ref_amb": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb", + "PreProcessingForVariantDiscovery_GATK4.ref_bwt": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt", + "PreProcessingForVariantDiscovery_GATK4.ref_ann": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann", + "PreProcessingForVariantDiscovery_GATK4.ref_pac": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac", + + "PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf", + "PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx", + "PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [ + "s3://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", + "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz" + ], + "PreProcessingForVariantDiscovery_GATK4.known_indels_sites_indices": [ + "s3://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi", + "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi" + ] + + +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl b/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl new file mode 100644 index 00000000..1c4ad8c8 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl @@ -0,0 +1,719 @@ +version 1.0 + +## Copyright Broad Institute, 2021 +## +## This WDL pipeline implements data pre-processing according to the GATK Best Practices. +## +## Requirements/expectations : +## - Pair-end sequencing data in unmapped BAM (uBAM) format +## - One or more read groups, one per uBAM file, all belonging to a single sample (SM) +## - Input uBAM files must additionally comply with the following requirements: +## - - filenames all have the same suffix (we use ".unmapped.bam") +## - - files must pass validation by ValidateSamFile +## - - reads are provided in query-sorted order +## - - all reads must have an RG tag +## +## Output : +## - A clean BAM file and its index, suitable for variant discovery analyses. +## +## Software version requirements +## - GATK 4 or later +## - BWA 0.7.15-r1140 +## - Picard 2.16.0-SNAPSHOT +## - Samtools 1.3.1 (using htslib 1.3.1) +## - Python 2.7 +## +## Cromwell version support +## - Successfully tested on v59 +## +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. Please see the dockers +## for detailed licensing information pertaining to the included programs. + +# WORKFLOW DEFINITION +workflow PreProcessingForVariantDiscovery_GATK4 { + input { + String sample_name + String ref_name + + File flowcell_unmapped_bams_list + String unmapped_bam_suffix + + File ref_fasta + File ref_fasta_index + File ref_dict + File? ref_alt + File ref_sa + File ref_ann + File ref_bwt + File ref_pac + File ref_amb + File dbSNP_vcf + File dbSNP_vcf_index + Array[File] known_indels_sites_VCFs + Array[File] known_indels_sites_indices + + String bwa_commandline = "bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta" + Int compression_level = 5 + + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.2.0.0" + String gatk_path = "/gatk/gatk" + String gotc_docker = "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.7-1603303710" + String gotc_path = "/usr/gitc/" + String python_docker = "python:2.7" + + Int flowcell_small_disk = 100 + Int flowcell_medium_disk = 200 + Int agg_small_disk = 200 + Int agg_medium_disk = 300 + Int agg_large_disk = 400 + + Int retry_attempts = 3 + } + String base_file_name = sample_name + "." + ref_name + + Array[File] flowcell_unmapped_bams = read_lines(flowcell_unmapped_bams_list) + + # Get the version of BWA to include in the PG record in the header of the BAM produced + # by MergeBamAlignment. + call GetBwaVersion { + input: + docker_image = gotc_docker, + bwa_path = gotc_path, + retry_attempts = retry_attempts + } + + # Align flowcell-level unmapped input bams in parallel + scatter (unmapped_bam in flowcell_unmapped_bams) { + + # Get the basename, i.e. strip the filepath and the extension + String bam_basename = basename(unmapped_bam, unmapped_bam_suffix) + + # Map reads to reference + call SamToFastqAndBwaMem { + input: + input_bam = unmapped_bam, + bwa_commandline = bwa_commandline, + output_bam_basename = bam_basename + ".unmerged", + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + ref_dict = ref_dict, + ref_alt = ref_alt, + ref_sa = ref_sa, + ref_ann = ref_ann, + ref_bwt = ref_bwt, + ref_pac = ref_pac, + ref_amb = ref_amb, + docker_image = gotc_docker, + bwa_path = gotc_path, + gotc_path = gotc_path, + disk_size = flowcell_medium_disk, + retry_attempts = retry_attempts, + compression_level = compression_level + } + + # Merge original uBAM and BWA-aligned BAM + call MergeBamAlignment { + input: + unmapped_bam = unmapped_bam, + bwa_commandline = bwa_commandline, + bwa_version = GetBwaVersion.version, + aligned_bam = SamToFastqAndBwaMem.output_bam, + output_bam_basename = bam_basename + ".aligned.unsorted", + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + ref_dict = ref_dict, + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = flowcell_medium_disk, + retry_attempts = retry_attempts, + compression_level = compression_level + } + } + + # Aggregate aligned+merged flowcell BAM files and mark duplicates + # We take advantage of the tool's ability to take multiple BAM inputs and write out a single output + # to avoid having to spend time just merging BAM files. + call MarkDuplicates { + input: + input_bams = MergeBamAlignment.output_bam, + output_bam_basename = base_file_name + ".aligned.unsorted.duplicates_marked", + metrics_filename = base_file_name + ".duplicate_metrics", + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = agg_large_disk, + compression_level = compression_level, + retry_attempts = retry_attempts + } + + # Sort aggregated+deduped BAM file and fix tags + call SortAndFixTags { + input: + input_bam = MarkDuplicates.output_bam, + output_bam_basename = base_file_name + ".aligned.duplicate_marked.sorted", + ref_dict = ref_dict, + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = agg_large_disk, + retry_attempts = 0, + compression_level = compression_level + } + + # Create list of sequences for scatter-gather parallelization + call CreateSequenceGroupingTSV { + input: + ref_dict = ref_dict, + docker_image = python_docker, + retry_attempts = retry_attempts + } + + # Perform Base Quality Score Recalibration (BQSR) on the sorted BAM in parallel + scatter (subgroup in CreateSequenceGroupingTSV.sequence_grouping) { + # Generate the recalibration model by interval + call BaseRecalibrator { + input: + input_bam = SortAndFixTags.output_bam, + input_bam_index = SortAndFixTags.output_bam_index, + recalibration_report_filename = base_file_name + ".recal_data.csv", + sequence_group_interval = subgroup, + dbSNP_vcf = dbSNP_vcf, + dbSNP_vcf_index = dbSNP_vcf_index, + known_indels_sites_VCFs = known_indels_sites_VCFs, + known_indels_sites_indices = known_indels_sites_indices, + ref_dict = ref_dict, + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = agg_small_disk, + retry_attempts = retry_attempts + } + } + + # Merge the recalibration reports resulting from by-interval recalibration + call GatherBqsrReports { + input: + input_bqsr_reports = BaseRecalibrator.recalibration_report, + output_report_filename = base_file_name + ".recal_data.csv", + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = flowcell_small_disk, + retry_attempts = retry_attempts + } + + scatter (subgroup in CreateSequenceGroupingTSV.sequence_grouping_with_unmapped) { + + # Apply the recalibration model by interval + call ApplyBQSR { + input: + input_bam = SortAndFixTags.output_bam, + input_bam_index = SortAndFixTags.output_bam_index, + output_bam_basename = base_file_name + ".aligned.duplicates_marked.recalibrated", + recalibration_report = GatherBqsrReports.output_bqsr_report, + sequence_group_interval = subgroup, + ref_dict = ref_dict, + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = agg_small_disk, + retry_attempts = retry_attempts + } + } + + # Merge the recalibrated BAM files resulting from by-interval recalibration + call GatherBamFiles { + input: + input_bams = ApplyBQSR.recalibrated_bam, + output_bam_basename = base_file_name, + docker_image = gatk_docker, + gatk_path = gatk_path, + disk_size = agg_large_disk, + retry_attempts = retry_attempts, + compression_level = compression_level + } + + # Outputs that will be retained when execution is complete + output { + File duplication_metrics = MarkDuplicates.duplicate_metrics + File bqsr_report = GatherBqsrReports.output_bqsr_report + File analysis_ready_bam = GatherBamFiles.output_bam + File analysis_ready_bam_index = GatherBamFiles.output_bam_index + File analysis_ready_bam_md5 = GatherBamFiles.output_bam_md5 + } +} + +# TASK DEFINITIONS + +# Get version of BWA +task GetBwaVersion { + input { + Float mem_size_gb = 1 + Int retry_attempts + String docker_image + String bwa_path + } + + command { + # Not setting "set -o pipefail" here because /bwa has a rc=1 and we don't want to allow rc=1 to succeed + # because the sed may also fail with that error and that is something we actually want to fail on. + ~{bwa_path}bwa 2>&1 | \ + grep -e '^Version' | \ + sed 's/Version: //' + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + } + output { + String version = read_string(stdout()) + } +} + +# Read unmapped BAM, convert on-the-fly to FASTQ and stream to BWA MEM for alignment +task SamToFastqAndBwaMem { + # This is the .alt file from bwa-kit (/~https://github.com/lh3/bwa/tree/master/bwakit), + # listing the reference contigs that are "alternative". Leave blank in JSON for legacy + # references such as b37 and hg19. + input { + File input_bam + String bwa_commandline + String output_bam_basename + File ref_fasta + File ref_fasta_index + File ref_dict + File? ref_alt + File ref_amb + File ref_ann + File ref_bwt + File ref_pac + File ref_sa + + Float mem_size_gb = 14 + String num_cpu = 16 + + Int compression_level + Int retry_attempts + Int disk_size + + String docker_image + String bwa_path + String gotc_path + } + Int command_mem_gb = ceil(mem_size_gb/2) + + command { + set -o pipefail + set -e + + # set the bash variable needed for the command-line + bash_ref_fasta=~{ref_fasta} + + java -Dsamjdk.compression_level=~{compression_level} -Xms~{command_mem_gb}G -jar ~{gotc_path}picard.jar \ + SamToFastq \ + INPUT=~{input_bam} \ + FASTQ=/dev/stdout \ + INTERLEAVE=true \ + NON_PF=true \ + | \ + ~{bwa_path}~{bwa_commandline} /dev/stdin - 2> >(tee ~{output_bam_basename}.bwa.stderr.log >&2) \ + | \ + samtools view -1 - > ~{output_bam_basename}.bam + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + cpu: num_cpu + disks: "local-disk " + disk_size + " HDD" + } + output { + File output_bam = "~{output_bam_basename}.bam" + File bwa_stderr_log = "~{output_bam_basename}.bwa.stderr.log" + } +} + +# Merge original input uBAM file with BWA-aligned BAM file +task MergeBamAlignment { + input { + File unmapped_bam + String bwa_commandline + String bwa_version + File aligned_bam + String output_bam_basename + File ref_fasta + File ref_fasta_index + File ref_dict + + Int compression_level + Int retry_attempts + Int disk_size + Float mem_size_gb = 4 + + String docker_image + String gatk_path + } + Int command_mem_gb = ceil(mem_size_gb) - 1 + + command { + # set the bash variable needed for the command-line + bash_ref_fasta=~{ref_fasta} + ~{gatk_path} --java-options "-Dsamjdk.compression_level=~{compression_level} -Xms~{command_mem_gb}G" \ + MergeBamAlignment \ + --VALIDATION_STRINGENCY SILENT \ + --EXPECTED_ORIENTATIONS FR \ + --ATTRIBUTES_TO_RETAIN X0 \ + --ALIGNED_BAM ~{aligned_bam} \ + --UNMAPPED_BAM ~{unmapped_bam} \ + --OUTPUT ~{output_bam_basename}.bam \ + --REFERENCE_SEQUENCE ~{ref_fasta} \ + --PAIRED_RUN true \ + --SORT_ORDER "unsorted" \ + --IS_BISULFITE_SEQUENCE false \ + --ALIGNED_READS_ONLY false \ + --CLIP_ADAPTERS false \ + --MAX_RECORDS_IN_RAM 2000000 \ + --ADD_MATE_CIGAR true \ + --MAX_INSERTIONS_OR_DELETIONS -1 \ + --PRIMARY_ALIGNMENT_STRATEGY MostDistant \ + --PROGRAM_RECORD_ID "bwamem" \ + --PROGRAM_GROUP_VERSION "~{bwa_version}" \ + --PROGRAM_GROUP_COMMAND_LINE "~{bwa_commandline}" \ + --PROGRAM_GROUP_NAME "bwamem" \ + --UNMAPPED_READ_STRATEGY COPY_TO_TAG \ + --ALIGNER_PROPER_PAIR_FLAGS true \ + --UNMAP_CONTAMINANT_READS true + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File output_bam = "~{output_bam_basename}.bam" + } +} + +# Sort BAM file by coordinate order and fix tag values for NM and UQ +task SortAndFixTags { + input { + File input_bam + String output_bam_basename + File ref_dict + File ref_fasta + File ref_fasta_index + + Int compression_level + Int retry_attempts + Int disk_size + Float mem_size_gb = 10 + + String docker_image + String gatk_path + } + Int command_mem_gb_sort = ceil(mem_size_gb) - 1 + Int command_mem_gb_fix = ceil((mem_size_gb - 1)/10) + + command { + set -o pipefail + + ~{gatk_path} --java-options "-Dsamjdk.compression_level=~{compression_level} -Xms~{command_mem_gb_sort}G" \ + SortSam \ + --INPUT ~{input_bam} \ + --OUTPUT /dev/stdout \ + --SORT_ORDER "coordinate" \ + --CREATE_INDEX false \ + --CREATE_MD5_FILE false \ + | \ + ~{gatk_path} --java-options "-Dsamjdk.compression_level=~{compression_level} -Xms~{command_mem_gb_fix}G" \ + SetNmMdAndUqTags \ + --INPUT /dev/stdin \ + --OUTPUT ~{output_bam_basename}.bam \ + --CREATE_INDEX true \ + --CREATE_MD5_FILE true \ + --REFERENCE_SEQUENCE ~{ref_fasta} + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File output_bam = "~{output_bam_basename}.bam" + File output_bam_index = "~{output_bam_basename}.bai" + File output_bam_md5 = "~{output_bam_basename}.bam.md5" + } +} + +# Mark duplicate reads to avoid counting non-independent observations +task MarkDuplicates { + input { + Array[File] input_bams + String output_bam_basename + String metrics_filename + + Int compression_level + Int retry_attempts + Int disk_size + Float mem_size_gb = 7.5 + + String docker_image + String gatk_path + } + Int command_mem_gb = ceil(mem_size_gb) - 2 + # Task is assuming query-sorted input so that the Secondary and Supplementary reads get marked correctly. + # This works because the output of BWA is query-grouped and therefore, so is the output of MergeBamAlignment. + # While query-grouped isn't actually query-sorted, it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname" + command { + ~{gatk_path} --java-options "-Dsamjdk.compression_level=~{compression_level} -Xms~{command_mem_gb}G" \ + MarkDuplicates \ + --INPUT ~{sep=' --INPUT ' input_bams} \ + --OUTPUT ~{output_bam_basename}.bam \ + --METRICS_FILE ~{metrics_filename} \ + --VALIDATION_STRINGENCY SILENT \ + --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 \ + --ASSUME_SORT_ORDER "queryname" \ + --CREATE_MD5_FILE true + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File output_bam = "~{output_bam_basename}.bam" + File duplicate_metrics = "~{metrics_filename}" + } +} + +# Generate sets of intervals for scatter-gathering over chromosomes +task CreateSequenceGroupingTSV { + input { + File ref_dict + + Int retry_attempts + Float mem_size_gb = 2 + + String docker_image + } + # Use python to create the Sequencing Groupings used for BQSR and PrintReads Scatter. + # It outputs to stdout where it is parsed into a wdl Array[Array[String]] + # e.g. [["1"], ["2"], ["3", "4"], ["5"], ["6", "7", "8"]] + command <<< + python <>> + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + } + output { + Array[Array[String]] sequence_grouping = read_tsv("sequence_grouping.txt") + Array[Array[String]] sequence_grouping_with_unmapped = read_tsv("sequence_grouping_with_unmapped.txt") + } +} + +# Generate Base Quality Score Recalibration (BQSR) model +task BaseRecalibrator { + input { + File input_bam + File input_bam_index + String recalibration_report_filename + Array[String] sequence_group_interval + File dbSNP_vcf + File dbSNP_vcf_index + Array[File] known_indels_sites_VCFs + Array[File] known_indels_sites_indices + File ref_dict + File ref_fasta + File ref_fasta_index + + Int retry_attempts + Int disk_size + Float mem_size_gb = 6 + + String docker_image + String gatk_path + } + Int command_mem_gb = ceil(mem_size_gb) - 2 + + command { + ~{gatk_path} --java-options "-Xms~{command_mem_gb}G" \ + BaseRecalibrator \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + --use-original-qualities \ + -O ~{recalibration_report_filename} \ + --known-sites ~{dbSNP_vcf} \ + --known-sites ~{sep=" --known-sites " known_indels_sites_VCFs} \ + -L ~{sep=" -L " sequence_group_interval} + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File recalibration_report = "~{recalibration_report_filename}" + } +} + +# Combine multiple recalibration tables from scattered BaseRecalibrator runs +# Note that when run from GATK 3.x the tool is not a walker and is invoked differently. +task GatherBqsrReports { + input { + Array[File] input_bqsr_reports + String output_report_filename + + Int retry_attempts + Int disk_size + Float mem_size_gb = 4 + + String docker_image + String gatk_path + } + Int command_mem_gb = ceil(mem_size_gb) - 1 + + command { + ~{gatk_path} --java-options "-Xms~{command_mem_gb}G" \ + GatherBQSRReports \ + -I ~{sep=' -I ' input_bqsr_reports} \ + -O ~{output_report_filename} + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File output_bqsr_report = "~{output_report_filename}" + } +} + +# Apply Base Quality Score Recalibration (BQSR) model +task ApplyBQSR { + input { + File input_bam + File input_bam_index + String output_bam_basename + File recalibration_report + Array[String] sequence_group_interval + File ref_dict + File ref_fasta + File ref_fasta_index + + Int retry_attempts + Int disk_size + Float mem_size_gb = 4 + + String docker_image + String gatk_path + } + Int command_mem_gb = ceil(mem_size_gb) - 1 + + command { + ~{gatk_path} --java-options "-Xms~{command_mem_gb}G" \ + ApplyBQSR \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + -O ~{output_bam_basename}.bam \ + -L ~{sep=" -L " sequence_group_interval} \ + -bqsr ~{recalibration_report} \ + --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \ + --add-output-sam-program-record \ + --create-output-bam-md5 \ + --use-original-qualities + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File recalibrated_bam = "~{output_bam_basename}.bam" + } +} + +# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs +task GatherBamFiles { + input { + Array[File] input_bams + String output_bam_basename + + Int compression_level + Int retry_attempts + Int disk_size + Float mem_size_gb = 3 + + String docker_image + String gatk_path + } + Int command_mem_gb = ceil(mem_size_gb) - 1 + + command { + ~{gatk_path} --java-options "-Dsamjdk.compression_level=~{compression_level} -Xms~{command_mem_gb}G" \ + GatherBamFiles \ + --INPUT ~{sep=' --INPUT ' input_bams} \ + --OUTPUT ~{output_bam_basename}.bam \ + --CREATE_INDEX true \ + --CREATE_MD5_FILE true + } + runtime { + awsBatchRetryAttempts: retry_attempts + docker: docker_image + memory: "~{mem_size_gb} GiB" + disks: "local-disk " + disk_size + " HDD" + } + output { + File output_bam = "~{output_bam_basename}.bam" + File output_bam_index = "~{output_bam_basename}.bai" + File output_bam_md5 = "~{output_bam_basename}.bam.md5" + } +} diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/MANIFEST.json new file mode 100644 index 00000000..8db42c9c --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "haplotypecaller-gvcf-gatk4.wdl", + "inputFileURLs": [ + "haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json b/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json new file mode 100644 index 00000000..c21f07bb --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json @@ -0,0 +1,10 @@ +{ + "HaplotypeCallerGvcf_GATK4.input_bam": "s3://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram", + "HaplotypeCallerGvcf_GATK4.input_bam_index": "s3://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.crai", + + "HaplotypeCallerGvcf_GATK4.ref_dict": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dict", + "HaplotypeCallerGvcf_GATK4.ref_fasta": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", + "HaplotypeCallerGvcf_GATK4.ref_fasta_index": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", + + "HaplotypeCallerGvcf_GATK4.scattered_calling_intervals_list": "s3://gatk-test-data/intervals/hg38_wgs_scattered_calling_intervals.txt" +} diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl b/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl new file mode 100644 index 00000000..49aad897 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl @@ -0,0 +1,264 @@ +version 1.0 + +## Copyright Broad Institute, 2019 +## +## The haplotypecaller-gvcf-gatk4 workflow runs the HaplotypeCaller tool +## from GATK4 in GVCF mode on a single sample according to GATK Best Practices. +## When executed the workflow scatters the HaplotypeCaller tool over a sample +## using an intervals list file. The output file produced will be a +## single gvcf file which can be used by the joint-discovery workflow. +## +## Requirements/expectations : +## - One analysis-ready BAM file for a single sample (as identified in RG:SM) +## - Set of variant calling intervals lists for the scatter, provided in a file +## +## Outputs : +## - One GVCF file and its index +## +## Cromwell version support +## - Successfully tested on v53 +## +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. Please see the dockers +## for detailed licensing information pertaining to the included programs. + +# WORKFLOW DEFINITION +workflow HaplotypeCallerGvcf_GATK4 { + input { + File input_bam + File input_bam_index + File ref_dict + File ref_fasta + File ref_fasta_index + File scattered_calling_intervals_list + + Boolean make_gvcf = true + Boolean make_bamout = false + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.2.0.0" + String gatk_path = "/gatk/gatk" + String gitc_docker = "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.7-1603303710" + String samtools_path = "samtools" + } + + Array[File] scattered_calling_intervals = read_lines(scattered_calling_intervals_list) + + #is the input a cram file? + Boolean is_cram = sub(basename(input_bam), ".*\\.", "") == "cram" + + String sample_basename = if is_cram then basename(input_bam, ".cram") else basename(input_bam, ".bam") + String vcf_basename = sample_basename + String output_suffix = if make_gvcf then ".g.vcf.gz" else ".vcf.gz" + String output_filename = vcf_basename + output_suffix + + # We need disk to localize the sharded input and output due to the scatter for HaplotypeCaller. + # If we take the number we are scattering by and reduce by 20 we will have enough disk space + # to account for the fact that the data is quite uneven across the shards. + Int potential_hc_divisor = length(scattered_calling_intervals) - 20 + Int hc_divisor = if potential_hc_divisor > 1 then potential_hc_divisor else 1 + + if ( is_cram ) { + call CramToBamTask { + input: + input_cram = input_bam, + sample_name = sample_basename, + ref_dict = ref_dict, + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + docker = gitc_docker, + samtools_path = samtools_path + } + } + + # Call variants in parallel over grouped calling intervals + scatter (interval_file in scattered_calling_intervals) { + + # Generate GVCF by interval + call HaplotypeCaller { + input: + input_bam = select_first([CramToBamTask.output_bam, input_bam]), + input_bam_index = select_first([CramToBamTask.output_bai, input_bam_index]), + interval_list = interval_file, + output_filename = output_filename, + ref_dict = ref_dict, + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + hc_scatter = hc_divisor, + make_gvcf = make_gvcf, + make_bamout = make_bamout, + docker = gatk_docker, + gatk_path = gatk_path + } + } + + # Merge per-interval GVCFs + call MergeGVCFs { + input: + input_vcfs = HaplotypeCaller.output_vcf, + input_vcfs_indexes = HaplotypeCaller.output_vcf_index, + output_filename = output_filename, + docker = gatk_docker, + gatk_path = gatk_path + } + + # Outputs that will be retained when execution is complete + output { + File output_vcf = MergeGVCFs.output_vcf + File output_vcf_index = MergeGVCFs.output_vcf_index + } +} + +# TASK DEFINITIONS + +task CramToBamTask { + input { + # Command parameters + File ref_fasta + File ref_fasta_index + File ref_dict + File input_cram + String sample_name + + # Runtime parameters + String docker + Int? machine_mem_gb + String samtools_path + Int? retry_attempts + } + + command { + set -e + set -o pipefail + + ~{samtools_path} view -h -T ~{ref_fasta} ~{input_cram} | + ~{samtools_path} view -b -o ~{sample_name}.bam - + ~{samtools_path} index -b ~{sample_name}.bam + mv ~{sample_name}.bam.bai ~{sample_name}.bai + } + runtime { + docker: docker + memory: select_first([machine_mem_gb, 15]) + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + output { + File output_bam = "~{sample_name}.bam" + File output_bai = "~{sample_name}.bai" + } +} + +# HaplotypeCaller per-sample in GVCF mode +task HaplotypeCaller { + input { + # Command parameters + File input_bam + File input_bam_index + File interval_list + String output_filename + File ref_dict + File ref_fasta + File ref_fasta_index + Float? contamination + Boolean make_gvcf + Boolean make_bamout + Int hc_scatter + + String? gcs_project_for_requester_pays + + String gatk_path + String? java_options + + # Runtime parameters + String docker + Int? mem_gb + Int? retry_attempts + } + + String java_opt = select_first([java_options, "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10"]) + + Int machine_mem_gb = select_first([mem_gb, 7]) + Int command_mem_gb = machine_mem_gb - 1 + + String vcf_basename = if make_gvcf then basename(output_filename, ".gvcf") else basename(output_filename, ".vcf") + String bamout_arg = if make_bamout then "-bamout ~{vcf_basename}.bamout.bam" else "" + + parameter_meta { + input_bam: { + description: "a bam file", + localization_optional: true + } + input_bam_index: { + description: "an index file for the bam input", + localization_optional: true + } + } + command { + set -e + + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}G ~{java_opt}" \ + HaplotypeCaller \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + -L ~{interval_list} \ + -O ~{output_filename} \ + -contamination ~{default="0" contamination} \ + -G StandardAnnotation -G StandardHCAnnotation ~{true="-G AS_StandardAnnotation" false="" make_gvcf} \ + -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90 \ + ~{true="-ERC GVCF" false="" make_gvcf} \ + ~{if defined(gcs_project_for_requester_pays) then "--gcs-project-for-requester-pays ~{gcs_project_for_requester_pays}" else ""} \ + ~{bamout_arg} + + # Cromwell doesn't like optional task outputs, so we have to touch this file. + touch ~{vcf_basename}.bamout.bam + } + runtime { + docker: docker + memory: machine_mem_gb + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + output { + File output_vcf = "~{output_filename}" + File output_vcf_index = "~{output_filename}.tbi" + File bamout = "~{vcf_basename}.bamout.bam" + } +} +# Merge GVCFs generated per-interval for the same sample +task MergeGVCFs { + input { + # Command parameters + Array[File] input_vcfs + Array[File] input_vcfs_indexes + String output_filename + + String gatk_path + + # Runtime parameters + String docker + Int? mem_gb + Int? retry_attempts + } + Int machine_mem_gb = select_first([mem_gb, 3]) + Int command_mem_gb = machine_mem_gb - 1 + + command { + set -e + + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}G" \ + MergeVcfs \ + --INPUT ~{sep=' --INPUT ' input_vcfs} \ + --OUTPUT ~{output_filename} + } + runtime { + docker: docker + memory: machine_mem_gb + " GB" + awsBatchRetryAttempts: select_first([retry_attempts, 3]) + } + output { + File output_vcf = "~{output_filename}" + File output_vcf_index = "~{output_filename}.tbi" + } +} + diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/MANIFEST.json new file mode 100644 index 00000000..2a377473 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/MANIFEST.json @@ -0,0 +1,5 @@ +{ + "mainWorkflowURL": "gatk4-rnaseq-germline-snps-indels.wdl", + "inputFileURLs": [ "gatk4-rnaseq-germline-snps-indels.inputs.json" ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.inputs.json b/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.inputs.json new file mode 100644 index 00000000..9f9285cf --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.inputs.json @@ -0,0 +1,20 @@ +{ + "RNAseq.inputBam": "s3://healthai-public-assets-us-east-1/agc-demo-data/rna_bam/NA12878_b37/NA12878.unmapped.bam", + + "RNAseq.refFasta": "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta", + "RNAseq.refFastaIndex": "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai", + "RNAseq.refDict": "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dict", + + "RNAseq.dbSnpVcf": "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf", + "RNAseq.dbSnpVcfIndex": "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf.idx", + "RNAseq.knownVcfs": [ + "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf", + "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf" + ], + "RNAseq.knownVcfsIndices": [ + "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx", + "s3://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf.idx" + ], + "RNAseq.annotationsGTF": "s3://gatk-test-data/intervals/star.gencode.v19.transcripts.patched_contigs.gtf" + +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.wdl b/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.wdl new file mode 100644 index 00000000..13d507c6 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.wdl @@ -0,0 +1,800 @@ +## Copyright Broad Institute, 2019 +## +## Workflows for processing RNA data for germline short variant discovery with GATK (v4) and related tools +## +## Requirements/expectations : +## - BAM +## +## Output : +## - A BAM file and its index. +## - A VCF file and its index. +## - A Filtered VCF file and its index. +## +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## For program versions, see docker containers. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. Please see the docker +## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed +## licensing information pertaining to the included programs. +version 1.0 + + +workflow RNAseq { + input { + Int? haplotypeScatterCount + File? zippedStarReferences + File annotationsGTF + File dbSnpVcfIndex + String? star_docker_override + File inputBam + String? gatk_path_override + Array[File] knownVcfs + File dbSnpVcf + String? gatk4_docker_override + File refFasta + Int? preemptible_tries + File refDict + File refFastaIndex + Int? minConfidenceForVariantCalling + Int? readLength + Array[File] knownVcfsIndices + } + String star_docker = select_first([star_docker_override, "quay.io/humancellatlas/secondary-analysis-star:v0.2.2-2.5.3a-40ead6e"]) + String gatk4_docker = select_first([gatk4_docker_override, "broadinstitute/gatk:latest"]) + File starReferences = select_first([zippedStarReferences, StarGenerateReferences.star_genome_refs_zipped, ""]) + String sampleName = basename(inputBam, ".bam") + String gatk_path = select_first([gatk_path_override, "/gatk/gatk"]) + Int preemptible_count = select_first([preemptible_tries, 3]) + Int scatterCount = select_first([haplotypeScatterCount, 6]) + if (!defined(zippedStarReferences)) { + call StarGenerateReferences { + input: + ref_fasta = refFasta, + ref_fasta_index = refFastaIndex, + annotations_gtf = annotationsGTF, + read_length = readLength, + docker = star_docker, + preemptible_count = preemptible_count + } + } + scatter (interval in ScatterIntervalList.out) { + File HaplotypeCallerOutputVcfIndex = HaplotypeCaller.output_vcf_index + File HaplotypeCallerOutputVcf = HaplotypeCaller.output_vcf + call HaplotypeCaller { + input: + input_bam = ApplyBQSR.output_bam, + input_bam_index = ApplyBQSR.output_bam_index, + base_name = sampleName + ".hc", + interval_list = interval, + ref_dict = refDict, + ref_fasta = refFasta, + ref_fasta_index = refFastaIndex, + dbSNP_vcf = dbSnpVcf, + dbSNP_vcf_index = dbSnpVcfIndex, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count, + stand_call_conf = minConfidenceForVariantCalling + } + } + call ScatterIntervalList { + input: + interval_list = gtfToCallingIntervals.interval_list, + scatter_count = scatterCount, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call ApplyBQSR { + input: + input_bam = SplitNCigarReads.output_bam, + input_bam_index = SplitNCigarReads.output_bam_index, + base_name = sampleName + ".aligned.duplicates_marked.recalibrated", + recalibration_report = BaseRecalibrator.recalibration_report, + ref_dict = refDict, + ref_fasta = refFasta, + ref_fasta_index = refFastaIndex, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call gtfToCallingIntervals { + input: + gtf = annotationsGTF, + ref_dict = refDict, + docker = gatk4_docker, + gatk_path = gatk_path, + preemptible_count = preemptible_count + } + call MergeBamAlignment { + input: + ref_fasta = refFasta, + ref_dict = refDict, + unaligned_bam = RevertSam.output_bam, + star_bam = StarAlign.output_bam, + base_name = ".merged", + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call StarAlign { + input: + star_genome_refs_zipped = starReferences, + fastq1 = SamToFastq.fastq1, + fastq2 = SamToFastq.fastq2, + base_name = sampleName + ".star", + read_length = readLength, + docker = star_docker, + preemptible_count = preemptible_count + } + call SamToFastq { + input: + unmapped_bam = RevertSam.output_bam, + base_name = sampleName, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call MergeVCFs { + input: + input_vcfs = HaplotypeCallerOutputVcf, + input_vcfs_indexes = HaplotypeCallerOutputVcfIndex, + output_vcf_name = sampleName + ".g.vcf.gz", + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call SplitNCigarReads { + input: + input_bam = MarkDuplicates.output_bam, + input_bam_index = MarkDuplicates.output_bam_index, + base_name = sampleName + ".split", + ref_fasta = refFasta, + ref_fasta_index = refFastaIndex, + ref_dict = refDict, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call MarkDuplicates { + input: + input_bam = MergeBamAlignment.output_bam, + base_name = sampleName + ".dedupped", + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call VariantFiltration { + input: + input_vcf = MergeVCFs.output_vcf, + input_vcf_index = MergeVCFs.output_vcf_index, + base_name = sampleName + ".variant_filtered.vcf.gz", + ref_dict = refDict, + ref_fasta = refFasta, + ref_fasta_index = refFastaIndex, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call BaseRecalibrator { + input: + input_bam = SplitNCigarReads.output_bam, + input_bam_index = SplitNCigarReads.output_bam_index, + recal_output_file = sampleName + ".recal_data.csv", + dbSNP_vcf = dbSnpVcf, + dbSNP_vcf_index = dbSnpVcfIndex, + known_indels_sites_VCFs = knownVcfs, + known_indels_sites_indices = knownVcfsIndices, + ref_dict = refDict, + ref_fasta = refFasta, + ref_fasta_index = refFastaIndex, + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + call RevertSam { + input: + input_bam = inputBam, + base_name = sampleName + ".reverted", + sort_order = "queryname", + gatk_path = gatk_path, + docker = gatk4_docker, + preemptible_count = preemptible_count + } + + output { + File variant_filtered_vcf_index = VariantFiltration.output_vcf_index + File merged_vcf = MergeVCFs.output_vcf + File merged_vcf_index = MergeVCFs.output_vcf_index + File variant_filtered_vcf = VariantFiltration.output_vcf + File recalibrated_bam_index = ApplyBQSR.output_bam_index + File recalibrated_bam = ApplyBQSR.output_bam + } +} +task MarkDuplicates { + input { + File input_bam + String base_name + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_bam = "${base_name}.bam" + File output_bam_index = "${base_name}.bai" + File metrics_file = "${base_name}.metrics" + } + command <<< + + ~{gatk_path} \ + MarkDuplicates \ + --INPUT ~{input_bam} \ + --OUTPUT ~{base_name}.bam \ + --CREATE_INDEX true \ + --VALIDATION_STRINGENCY SILENT \ + --METRICS_FILE ~{base_name}.metrics + + >>> + runtime { + # disks: "local-disk " + sub(((size(input_bam, "GB") + 1) * 3), "\..*", "") + " HDD" + docker: docker + memory: "4 GB" + preemptible: preemptible_count + } + +} +task BaseRecalibrator { + input { + File input_bam + File input_bam_index + String recal_output_file + File dbSNP_vcf + File dbSNP_vcf_index + Array[File] known_indels_sites_VCFs + Array[File] known_indels_sites_indices + File ref_dict + File ref_fasta + File ref_fasta_index + String gatk_path + String docker + Int preemptible_count + } + + + output { + File recalibration_report = recal_output_file + } + command <<< + + ~{gatk_path} --java-options "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal \ + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails \ + -Xloggc:gc_log.log -Xms4000m" \ + BaseRecalibrator \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + --use-original-qualities \ + -O ~{recal_output_file} \ + -known-sites ~{dbSNP_vcf} \ + -known-sites ~{sep=" --known-sites " known_indels_sites_VCFs} + + >>> + runtime { + memory: "6 GB" + # disks: "local-disk " + sub((size(input_bam, "GB") * 3) + 30, "\..*", "") + " HDD" + docker: docker + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task RevertSam { + input { + File input_bam + String base_name + String sort_order + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_bam = "${base_name}.bam" + } + command <<< + + ~{gatk_path} \ + RevertSam \ + --INPUT ~{input_bam} \ + --OUTPUT ~{base_name}.bam \ + --VALIDATION_STRINGENCY SILENT \ + --ATTRIBUTE_TO_CLEAR FT \ + --ATTRIBUTE_TO_CLEAR CO \ + --SORT_ORDER ~{sort_order} + + >>> + runtime { + docker: docker + # disks: "local-disk " + sub(((size(input_bam, "GB") + 1) * 5), "\..*", "") + " HDD" + memory: "4 GB" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task ApplyBQSR { + input { + File input_bam + File input_bam_index + String base_name + File recalibration_report + File ref_dict + File ref_fasta + File ref_fasta_index + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_bam = "${base_name}.bam" + File output_bam_index = "${base_name}.bai" + } + command <<< + + ~{gatk_path} \ + --java-options "-XX:+PrintFlagsFinal -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps \ + -XX:+PrintGCDetails -Xloggc:gc_log.log \ + -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xms3000m" \ + ApplyBQSR \ + --add-output-sam-program-record \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + --use-original-qualities \ + -O ~{base_name}.bam \ + --bqsr-recal-file ~{recalibration_report} + + >>> + runtime { + memory: "3500 MB" + # disks: "local-disk " + sub((size(input_bam, "GB") * 4) + 30, "\..*", "") + " HDD" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + docker: docker + } + +} +task StarAlign { + input { + File star_genome_refs_zipped + File fastq1 + File fastq2 + String base_name + Int? read_length + Int length = select_first([read_length, 101]) + Int? num_threads + Int threads = select_first([num_threads, 8]) + Int? star_mem_max_gb + Int star_mem = select_first([star_mem_max_gb, 45]) + Int? star_limitOutSJcollapsed + #Int? additional_disk + #Int add_to_disk = select_first([additional_disk, 0]) + String docker + Int preemptible_count + } + + + output { + File output_bam = "${base_name}.Aligned.sortedByCoord.out.bam" + File output_log_final = "${base_name}.Log.final.out" + File output_log = "${base_name}.Log.out" + File output_log_progress = "${base_name}.Log.progress.out" + File output_SJ = "${base_name}.SJ.out.tab" + } + command <<< + + set -e + + tar -xvzf ~{star_genome_refs_zipped} + + STAR \ + --genomeDir STAR2_5 \ + --runThreadN ~{threads} \ + --readFilesIn ~{fastq1} ~{fastq2} \ + --readFilesCommand "gunzip -c" \ + ~{"--sjdbOverhang " + (length - 1)} \ + --outSAMtype BAM SortedByCoordinate \ + --twopassMode Basic \ + --limitBAMsortRAM ~{star_mem + "000000000"} \ + --limitOutSJcollapsed ~{default="1000000" star_limitOutSJcollapsed} \ + --outFileNamePrefix ~{base_name}. + + >>> + runtime { + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + # disks: "local-disk " + sub(((size(fastq1, "GB") + size(fastq2, "GB") * 10) + 30 + add_to_disk), "\..*", "") + " HDD" + docker: docker + cpu: threads + memory: (star_mem + 1) + " GB" + } + +} +task MergeVCFs { + input { + Array[File] input_vcfs + Array[File] input_vcfs_indexes + String output_vcf_name + #Int? disk_size = 5 + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_vcf = output_vcf_name + File output_vcf_index = "${output_vcf_name}.tbi" + } + command <<< + + ~{gatk_path} --java-options "-Xms2000m" \ + MergeVcfs \ + --INPUT ~{sep=" --INPUT " input_vcfs} \ + --OUTPUT ~{output_vcf_name} + + >>> + runtime { + memory: "3 GB" + # disks: "local-disk " + disk_size + " HDD" + docker: docker + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task VariantFiltration { + input { + File input_vcf + File input_vcf_index + String base_name + File ref_dict + File ref_fasta + File ref_fasta_index + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_vcf = "${base_name}" + File output_vcf_index = "${base_name}.tbi" + } + command <<< + + ~{gatk_path} \ + VariantFiltration \ + --R ~{ref_fasta} \ + --V ~{input_vcf} \ + --window 35 \ + --cluster 3 \ + --filter-name "FS" \ + --filter "FS > 30.0" \ + --filter-name "QD" \ + --filter "QD < 2.0" \ + -O ~{base_name} + + >>> + runtime { + docker: docker + memory: "3 GB" + # disks: "local-disk " + sub((size(input_vcf, "GB") * 2) + 30, "\..*", "") + " HDD" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task gtfToCallingIntervals { + input { + File gtf + File ref_dict + String output_name = basename(gtf, ".gtf") + ".exons.interval_list" + String docker + String gatk_path + Int preemptible_count + } + + + output { + File interval_list = "${output_name}" + } + command <<< + + + set -e + + Rscript --no-save -<<'RCODE' + gtf = read.table("~{gtf}", sep="\t") + gtf = subset(gtf, V3 == "exon") + write.table(data.frame(chrom=gtf[,'V1'], start=gtf[,'V4'], end=gtf[,'V5']), "exome.bed", quote = F, sep="\t", col.names = F, row.names = F) + RCODE + + awk '{print $1 "\t" ($2 - 1) "\t" $3}' exome.bed > exome.fixed.bed + + ~{gatk_path} \ + BedToIntervalList \ + -I exome.fixed.bed \ + -O ~{output_name} \ + -SD ~{ref_dict} + + >>> + runtime { + docker: docker + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task ScatterIntervalList { + input { + File interval_list + Int scatter_count + String gatk_path + String docker + Int preemptible_count + } + + + output { + Array[File] out = glob("out/*/*.interval_list") + Int interval_count = read_int("interval_count.txt") + } + command <<< + + set -e + mkdir out + ~{gatk_path} --java-options "-Xms1g" \ + IntervalListTools \ + --SCATTER_COUNT ~{scatter_count} \ + --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \ + --UNIQUE true \ + --SORT true \ + --INPUT ~{interval_list} \ + --OUTPUT out + + python3 <>> + runtime { + # disks: "local-disk 1 HDD" + memory: "2 GB" + docker: docker + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task MergeBamAlignment { + input { + File ref_fasta + File ref_dict + File unaligned_bam + File star_bam + String base_name + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_bam = "${base_name}.bam" + } + command <<< + + ~{gatk_path} \ + MergeBamAlignment \ + --REFERENCE_SEQUENCE ~{ref_fasta} \ + --UNMAPPED_BAM ~{unaligned_bam} \ + --ALIGNED_BAM ~{star_bam} \ + --OUTPUT ~{base_name}.bam \ + --INCLUDE_SECONDARY_ALIGNMENTS false \ + --VALIDATION_STRINGENCY SILENT + + >>> + runtime { + docker: docker + # disks: "local-disk " + sub(((size(unaligned_bam, "GB") + size(star_bam, "GB") + 1) * 5), "\..*", "") + " HDD" + memory: "4 GB" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task SplitNCigarReads { + input { + File input_bam + File input_bam_index + String base_name + File ref_fasta + File ref_fasta_index + File ref_dict + String gatk_path + String docker + Int preemptible_count + } + + + output { + File output_bam = "${base_name}.bam" + File output_bam_index = "${base_name}.bai" + } + command <<< + + ~{gatk_path} \ + SplitNCigarReads \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + -O ~{base_name}.bam + + >>> + runtime { + # disks: "local-disk " + sub(((size(input_bam, "GB") + 1) * 5 + size(ref_fasta, "GB")), "\..*", "") + " HDD" + docker: docker + memory: "4 GB" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task HaplotypeCaller { + input { + File input_bam + File input_bam_index + String base_name + File interval_list + File ref_dict + File ref_fasta + File ref_fasta_index + File dbSNP_vcf + File dbSNP_vcf_index + String gatk_path + String docker + Int preemptible_count + Int? stand_call_conf + } + + + output { + File output_vcf = "${base_name}.vcf.gz" + File output_vcf_index = "${base_name}.vcf.gz.tbi" + } + command <<< + + ~{gatk_path} --java-options "-Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \ + HaplotypeCaller \ + -R ~{ref_fasta} \ + -I ~{input_bam} \ + -L ~{interval_list} \ + -O ~{base_name}.vcf.gz \ + -dont-use-soft-clipped-bases \ + --standard-min-confidence-threshold-for-calling ~{default="20" stand_call_conf} \ + --dbsnp ~{dbSNP_vcf} + + >>> + runtime { + docker: docker + memory: "6.5 GB" + # disks: "local-disk " + sub((size(input_bam, "GB") * 2) + 30, "\..*", "") + " HDD" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task SamToFastq { + input { + File unmapped_bam + String base_name + String gatk_path + String docker + Int preemptible_count + } + + + output { + File fastq1 = "${base_name}.1.fastq.gz" + File fastq2 = "${base_name}.2.fastq.gz" + } + command <<< + + ~{gatk_path} \ + SamToFastq \ + --INPUT ~{unmapped_bam} \ + --VALIDATION_STRINGENCY SILENT \ + --FASTQ ~{base_name}.1.fastq.gz \ + --SECOND_END_FASTQ ~{base_name}.2.fastq.gz + + >>> + runtime { + docker: docker + memory: "4 GB" + # disks: "local-disk " + sub(((size(unmapped_bam, "GB") + 1) * 5), "\..*", "") + " HDD" + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + } + +} +task StarGenerateReferences { + input { + File ref_fasta + File ref_fasta_index + File annotations_gtf + Int? read_length + Int length = select_first([read_length, 101]) + Int? num_threads + Int threads = select_first([num_threads, 8]) + #Int? additional_disk + #Int add_to_disk = select_first([additional_disk, 0]) + #Int disk_size = select_first([100 + add_to_disk, 100]) + Int? mem_gb + Int mem = select_first([100, mem_gb]) + String docker + Int preemptible_count + } + + + output { + Array[File] star_logs = glob("*.out") + File star_genome_refs_zipped = "star-HUMAN-refs.tar.gz" + } + command <<< + + set -e + mkdir STAR2_5 + + STAR \ + --runMode genomeGenerate \ + --genomeDir STAR2_5 \ + --genomeFastaFiles ~{ref_fasta} \ + --sjdbGTFfile ~{annotations_gtf} \ + ~{"--sjdbOverhang " + (length - 1)} \ + --runThreadN ~{threads} + + ls STAR2_5 + + tar -zcvf star-HUMAN-refs.tar.gz STAR2_5 + + >>> + runtime { + preemptible: preemptible_count + awsBatchRetryAttempts: preemptible_count + # disks: "local-disk " + disk_size + " HDD" + docker: docker + cpu: threads + memory: mem + " GB" + } + +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/MANIFEST.json new file mode 100644 index 00000000..039a7907 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "bam-to-unmapped-bams.wdl", + "inputFileURLs": [ + "bam-to-unmapped-bams.inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.inputs.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.inputs.json new file mode 100644 index 00000000..3a203d02 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.inputs.json @@ -0,0 +1,3 @@ +{ + "BamToUnmappedBams.input_bam": "s3://gatk-test-data/wgs_bam/NA12878_20k_hg38/NA12878.bam" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.wdl b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.wdl new file mode 100644 index 00000000..a60ffe8b --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.wdl @@ -0,0 +1,129 @@ +version 1.0 +## Copyright Broad Institute, 2018 +## +## This WDL converts BAM to unmapped BAMs +## +## Requirements/expectations : +## - BAM file +## +## Outputs : +## - Sorted Unmapped BAMs +## +## Cromwell version support +## - Successfully tested on v47 +## - Does not work on versions < v23 due to output syntax +## +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## For program versions, see docker containers. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. Please see the docker +## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed +## licensing information pertaining to the included programs. + +# WORKFLOW DEFINITION +workflow BamToUnmappedBams { + input { + File input_bam + + Int additional_disk_size = 20 + String gatk_docker = "public.ecr.aws/aws-genomics/broadinstitute/gatk:4.1.9.0" + String gatk_path = "/gatk/gatk" + } + + call RevertSam { + input: + input_bam = input_bam, + docker = gatk_docker, + gatk_path = gatk_path + } + + scatter (unmapped_bam in RevertSam.unmapped_bams) { + String output_basename = basename(unmapped_bam, ".coord.sorted.unmapped.bam") + + call SortSam { + input: + input_bam = unmapped_bam, + sorted_bam_name = output_basename + ".unmapped.bam", + docker = gatk_docker, + gatk_path = gatk_path + } + } + + output { + Array[File] output_bams = SortSam.sorted_bam + } +} + +task RevertSam { + input { + #Command parameters + File input_bam + String gatk_path + + #Runtime parameters + String docker + Int machine_mem_gb = 2 + Int preemptible_attempts = 3 + Int awsBatchRetryAttempts = 3 + } + Int command_mem_gb = machine_mem_gb - 1 ####Needs to occur after machine_mem_gb is set + + command { + + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}g" \ + RevertSam \ + --INPUT ~{input_bam} \ + --OUTPUT ./ \ + --OUTPUT_BY_READGROUP true \ + --VALIDATION_STRINGENCY LENIENT \ + --ATTRIBUTE_TO_CLEAR FT \ + --ATTRIBUTE_TO_CLEAR CO \ + --SORT_ORDER coordinate + } + runtime { + docker: docker + memory: machine_mem_gb + " GB" + preemptible: preemptible_attempts + awsBatchRetryAttempts: awsBatchRetryAttempts + } + output { + Array[File] unmapped_bams = glob("*.bam") + } +} + +task SortSam { + input { + #Command parameters + File input_bam + String sorted_bam_name + #Runtime parameters + String gatk_path + String docker + Int machine_mem_gb = 4 + Int preemptible_attempts = 3 + Int awsBatchRetryAttempts = 3 + } + Int command_mem_gb = machine_mem_gb - 1 ####Needs to occur after machine_mem_gb is set + + command { + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}g" \ + SortSam \ + --INPUT ~{input_bam} \ + --OUTPUT ~{sorted_bam_name} \ + --SORT_ORDER queryname \ + --MAX_RECORDS_IN_RAM 1000000 + } + runtime { + docker: docker + memory: machine_mem_gb + " GB" + preemptible: preemptible_attempts + awsBatchRetryAttempts: awsBatchRetryAttempts + } + output { + File sorted_bam = "~{sorted_bam_name}" + } +} diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/MANIFEST.json new file mode 100644 index 00000000..d5649a88 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "cram-to-bam.wdl", + "inputFileURLs": [ + "cram-to-bam.inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.inputs.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.inputs.json new file mode 100644 index 00000000..107370fd --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.inputs.json @@ -0,0 +1,8 @@ +{ + "CramToBamFlow.sample_name": "NA12878", + "CramToBamFlow.input_cram": "s3://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram", + + "CramToBamFlow.ref_dict": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dict", + "CramToBamFlow.ref_fasta": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", + "CramToBamFlow.ref_fasta_index": "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.wdl b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.wdl new file mode 100644 index 00000000..42470600 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.wdl @@ -0,0 +1,144 @@ +version 1.0 +## Copyright Broad Institute, 2017 +## This script should convert a CRAM to SAM to BAM and output a BAM, BAM Index, and validation report to a Google bucket. If you'd like to do ## this on multiple CRAMS, create a sample set in the Data tab. +## The reason this approach was chosen instead of converting CRAM to BAM directly using Samtools is because Samtools 1.3 produces incorrect +## bins due to an old version of htslib included in the package. Samtools versions 1.4 & 1.5 have an NM issue that causes them to not validate ## with Picard. +## +## TESTED: It was tested using the Genomes in the Cloud Docker image version 2.3.1-1500064817. +## Versions of other tools on this image at the time of testing: +## PICARD_VER=1.1150 +## GATK34_VER=3.4-g3c929b0 +## GATK35_VER=3.5-0-g36282e4 +## GATK36_VER=3.6-44-ge7d1cd2 +## GATK4_VER=4.beta.1 +## SAMTOOLS_VER=1.3.1 +## BWA_VER=0.7.15.r1140 +## TABIX_VER=0.2.5_r1005 +## BGZIP_VER=1.3 +## SVTOOLKIT_VER=2.00-1650 +## It was tested pulling the HG38 reference Fasta and Fai. +## Successfully tested on Cromwell version 47. Does not work on versions < v23 due to output syntax +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## +## LICENSING : This script is released under the WDL source code license (BSD-3) (see LICENSE in /~https://github.com/broadinstitute/wdl). +## Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script. +## Please see the docker for detailed licensing information pertaining to the included programs. +## +#WORKFLOW DEFINITION +workflow CramToBamFlow { + input { + File ref_fasta + File ref_fasta_index + File ref_dict + File input_cram + String sample_name + String gotc_docker = "public.ecr.aws/aws-genomics/broadinstitute/genomes-in-the-cloud:2.4.7-1603303710" + Int preemptible_tries = 3 + } + + #converts CRAM to SAM to BAM and makes BAI + call CramToBamTask{ + input: + ref_fasta = ref_fasta, + ref_fasta_index = ref_fasta_index, + ref_dict = ref_dict, + input_cram = input_cram, + sample_name = sample_name, + docker_image = gotc_docker, + preemptible_tries = preemptible_tries + } + + #validates Bam + call ValidateSamFile{ + input: + input_bam = CramToBamTask.outputBam, + docker_image = gotc_docker, + preemptible_tries = preemptible_tries + } + + #Outputs Bam, Bai, and validation report to the FireCloud data model + output { + File outputBam = CramToBamTask.outputBam + File outputBai = CramToBamTask.outputBai + File validation_report = ValidateSamFile.report + } + +} + +#Task Definitions +task CramToBamTask { + input { + # Command parameters + File ref_fasta + File ref_fasta_index + File ref_dict + File input_cram + String sample_name + + # Runtime parameters + Int machine_mem_size = 15 + String docker_image + Int preemptible_tries + } + + #Calls samtools view to do the conversion + command { + set -eo pipefail + + samtools view -h -T ~{ref_fasta} ~{input_cram} | + samtools view -b -o ~{sample_name}.bam - + samtools index -b ~{sample_name}.bam + mv ~{sample_name}.bam.bai ~{sample_name}.bai + } + + #Run time attributes: + #Use a docker with samtools. Set this up as a workspace attribute. + #cpu of one because no multi-threading is required. This is also default, so don't need to specify. + #disk_size should equal input size + output size + buffer + runtime { + docker: docker_image + memory: machine_mem_size + " GB" + preemptible: preemptible_tries + awsBatchRetryAttempts: preemptible_tries + } + + #Outputs a BAM and BAI with the same sample name + output { + File outputBam = "~{sample_name}.bam" + File outputBai = "~{sample_name}.bai" + } +} + +#Validates BAM output to ensure it wasn't corrupted during the file conversion +task ValidateSamFile { + input { + File input_bam + Int machine_mem_size = 4 + String docker_image + Int preemptible_tries + } + String output_name = basename(input_bam, ".bam") + ".validation_report" + Int command_mem_size = machine_mem_size - 1 + command { + java -Xmx~{command_mem_size}G -jar /usr/gitc/picard.jar \ + ValidateSamFile \ + INPUT=~{input_bam} \ + OUTPUT=~{output_name} \ + MODE=SUMMARY \ + IS_BISULFITE_SEQUENCED=false + } + #Run time attributes: + #Use a docker with the picard.jar. Set this up as a workspace attribute. + #Read more about return codes here: /~https://github.com/broadinstitute/cromwell#continueonreturncode + runtime { + docker: docker_image + memory: machine_mem_size + " GB" + preemptible: preemptible_tries + awsBatchRetryAttempts: preemptible_tries + continueOnReturnCode: [0,1] + } + #A text file is generated that will list errors or warnings that apply. + output { + File report = "~{output_name}" + } +} diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/MANIFEST.json new file mode 100644 index 00000000..bbb5e7aa --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "interleaved-fastq-to-paired-fastq.wdl", + "inputFileURLs": [ + "interleaved-fastq-to-paired-fastq.inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.inputs.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.inputs.json new file mode 100644 index 00000000..c8244f27 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.inputs.json @@ -0,0 +1,3 @@ +{ + "UninterleaveFastqs.input_fastq": "s3://healthai-public-assets-us-east-1/agc-demo-data/interleaved-fastq/H06HDADXX130110.1.ATCACGAT.20k_reads.interleaved.fastq" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.wdl b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.wdl new file mode 100644 index 00000000..ed5b3200 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.wdl @@ -0,0 +1,54 @@ +version 1.0 +# This WDL takes in a single interleaved(R1+R2) FASTQ file and separates it into +# separate R1 and R2 FASTQ (i.e. paired FASTQ) files. Paired FASTQ files are the +# input format for the tool that generates unmapped BAMs (the format used in most +# GATK processing and analysis tools). +# +# Requirements/expectations +# - Interleaved Fastq file +# +# Outputs +# - Separate R1 and R2 FASTQ files (i.e. paired FASTQ) +# +# LICENSING : This script is released under the WDL source code license (BSD-3) (see LICENSE in /~https://github.com/broadinstitute/wdl). +# Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script. +# Please see the docker for detailed licensing information pertaining to the included programs. +################## + +workflow UninterleaveFastqs { + input { + File input_fastq + } + + call uninterleave_fqs { + input: + input_fastq = input_fastq + } + +} + +task uninterleave_fqs { + input { + File input_fastq + + Int machine_mem_gb = 8 + } + String r1_name = basename(input_fastq, ".fastq") + "_reads_1.fastq" + String r2_name = basename(input_fastq, ".fastq") + "_reads_2.fastq" + + command { + cat ~{input_fastq} | paste - - - - - - - - | \ + tee >(cut -f 1-4 | tr "\t" "\n" > ~{r1_name}) | \ + cut -f 5-8 | tr "\t" "\n" > ~{r2_name} + } + + runtime { + docker: "public.ecr.aws/lts/ubuntu:20.04_stable" + memory: machine_mem_gb + " GB" + } + + output { + File r1_fastq = "~{r1_name}" + File r2_fastq = "~{r2_name}" + } +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/MANIFEST.json new file mode 100644 index 00000000..c2323ce6 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "paired-fastq-to-unmapped-bam.wdl", + "inputFileURLs": [ + "paired-fastq-to-unmapped-inputs.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-bam.wdl b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-bam.wdl new file mode 100644 index 00000000..b118c535 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-bam.wdl @@ -0,0 +1,158 @@ +version 1.0 +##Copyright Broad Institute, 2018 +## +## This WDL converts paired FASTQ to uBAM and adds read group information +## +## Requirements/expectations : +## - Pair-end sequencing data in FASTQ format (one file per orientation) +## - The following metada descriptors per sample: +## - readgroup +## - sample_name +## - library_name +## - platform_unit +## - run_date +## - platform_name +## - sequecing_center +## +## Outputs : +## - Set of unmapped BAMs, one per read group +## - File of a list of the generated unmapped BAMs +## +## Cromwell version support +## - Successfully tested on v47 +## - Does not work on versions < v23 due to output syntax +## +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## For program versions, see docker containers. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. Please see the docker +## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed +## licensing information pertaining to the included programs. + +# WORKFLOW DEFINITION +workflow ConvertPairedFastQsToUnmappedBamWf { + input { + String sample_name + File fastq_1 + File fastq_2 + String readgroup_name + String library_name + String platform_unit + String run_date + String platform_name + String sequencing_center + + Boolean make_fofn = false + + String gatk_docker = "public.ecr.aws/aws-genomics/broadinstitute/gatk:4.1.9.0" + String gatk_path = "/gatk/gatk" + + } + + String ubam_list_name = sample_name + + # Convert pair of FASTQs to uBAM + call PairedFastQsToUnmappedBAM { + input: + sample_name = sample_name, + fastq_1 = fastq_1, + fastq_2 = fastq_2, + readgroup_name = readgroup_name, + library_name = library_name, + platform_unit = platform_unit, + run_date = run_date, + platform_name = platform_name, + sequencing_center = sequencing_center, + gatk_path = gatk_path, + docker = gatk_docker, + } + + #Create a file with the generated ubam + if (make_fofn) { + call CreateFoFN { + input: + ubam = PairedFastQsToUnmappedBAM.output_unmapped_bam, + fofn_name = ubam_list_name + ".ubam" + } + } + + # Outputs that will be retained when execution is complete + output { + File output_unmapped_bam = PairedFastQsToUnmappedBAM.output_unmapped_bam + File? unmapped_bam_list = CreateFoFN.fofn_list + } +} + +# TASK DEFINITIONS + +# Convert a pair of FASTQs to uBAM +task PairedFastQsToUnmappedBAM { + input { + # Command parameters + String sample_name + File fastq_1 + File fastq_2 + String readgroup_name + String library_name + String platform_unit + String run_date + String platform_name + String sequencing_center + String gatk_path + + # Runtime parameters + Int machine_mem_gb = 7 + Int preemptible_attempts = 3 + String docker + } + Int command_mem_gb = machine_mem_gb - 1 + command { + ~{gatk_path} --java-options "-Xmx~{command_mem_gb}g" \ + FastqToSam \ + --FASTQ ~{fastq_1} \ + --FASTQ2 ~{fastq_2} \ + --OUTPUT ~{readgroup_name}.unmapped.bam \ + --READ_GROUP_NAME ~{readgroup_name} \ + --SAMPLE_NAME ~{sample_name} \ + --LIBRARY_NAME ~{library_name} \ + --PLATFORM_UNIT ~{platform_unit} \ + --RUN_DATE ~{run_date} \ + --PLATFORM ~{platform_name} \ + --SEQUENCING_CENTER ~{sequencing_center} + } + runtime { + docker: docker + memory: machine_mem_gb + " GB" + preemptible: preemptible_attempts + awsBatchRetryAttempts: preemptible_attempts + } + output { + File output_unmapped_bam = "~{readgroup_name}.unmapped.bam" + } +} + +# Creats a file of file names of the uBAM, which is a text file with each row having the path to the file. +# In this case there will only be one file path in the txt file but this format is used by +# the pre-processing for variant discvoery workflow. +task CreateFoFN { + input { + # Command parameters + String ubam + String fofn_name + } + command { + echo ~{ubam} > ~{fofn_name}.list + } + output { + File fofn_list = "~{fofn_name}.list" + } + runtime { + docker: "public.ecr.aws/lts/ubuntu:20.04_stable" + preemptible: 3 + awsBatchRetryAttempts: 3 + } +} diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-inputs.json b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-inputs.json new file mode 100644 index 00000000..7f7ab9da --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-inputs.json @@ -0,0 +1,13 @@ +{ + "ConvertPairedFastQsToUnmappedBamWf.readgroup_name": "NA12878_A", + "ConvertPairedFastQsToUnmappedBamWf.sample_name": "NA12878", + "ConvertPairedFastQsToUnmappedBamWf.fastq_1": "s3://gatk-test-data/wgs_fastq/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_1.fastq", + "ConvertPairedFastQsToUnmappedBamWf.fastq_2": "s3://gatk-test-data/wgs_fastq/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_2.fastq", + "ConvertPairedFastQsToUnmappedBamWf.library_name": "Solexa-NA12878", + "ConvertPairedFastQsToUnmappedBamWf.platform_unit": "H06HDADXX130110.2.ATCACGAT", + "ConvertPairedFastQsToUnmappedBamWf.run_date": "2016-09-01T02:00:00+0200", + "ConvertPairedFastQsToUnmappedBamWf.platform_name": "illumina", + "ConvertPairedFastQsToUnmappedBamWf.sequencing_center": "BI", + + "ConvertPairedFastQsToUnmappedBamWf.make_fofn": true +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-validation/MANIFEST.json b/examples/gatk-best-practices-project-miniwdl/seq-format-validation/MANIFEST.json new file mode 100644 index 00000000..21a685c2 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-validation/MANIFEST.json @@ -0,0 +1,7 @@ +{ + "mainWorkflowURL": "validate-bam.wdl", + "inputFileURLs": [ + "validate-bams.input.json" + ], + "engineOptions": "--no-cache" +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bam.wdl b/examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bam.wdl new file mode 100644 index 00000000..2bddca0c --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bam.wdl @@ -0,0 +1,90 @@ +version 1.0 +## Copyright Broad Institute, 2017 +## +## This WDL performs format validation on SAM/BAM files in a list +## +## Requirements/expectations : +## - One or more SAM or BAM files to validate +## - Explicit request of either SUMMARY or VERBOSE mode in inputs.json +## +## Outputs: +## - Set of .txt files containing the validation reports, one per input file +## +## Cromwell version support +## - Successfully tested on v32 +## - Does not work on versions < v23 due to output syntax +## +## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. +## For program versions, see docker containers. +## +## LICENSING : +## This script is released under the WDL source code license (BSD-3) (see LICENSE in +## /~https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## be subject to different licenses. Users are responsible for checking that they are +## authorized to run all programs before running this script. Please see the docker +## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed +## licensing information pertaining to the included programs. + +# WORKFLOW DEFINITION +workflow ValidateBamsWf { + input { + Array[File] bam_array + String gatk_docker = "public.ecr.aws/aws-genomics/broadinstitute/gatk:4.1.9.0" + String gatk_path = "/gatk/gatk" + } + + # Process the input files in parallel + scatter (input_bam in bam_array) { + + # Get the basename, i.e. strip the filepath and the extension + String bam_basename = basename(input_bam, ".bam") + + # Run the validation + call ValidateBAM { + input: + input_bam = input_bam, + output_basename = bam_basename + ".validation", + docker = gatk_docker, + gatk_path = gatk_path + } + } + + # Outputs that will be retained when execution is complete + output { + Array[File] validation_reports = ValidateBAM.validation_report + } +} + +# TASK DEFINITIONS + +# Validate a SAM or BAM using Picard ValidateSamFile +task ValidateBAM { + input { + # Command parameters + File input_bam + String output_basename + String? validation_mode + String gatk_path + + # Runtime parameters + String docker + Int machine_mem_gb = 4 + } + + String output_name = "${output_basename}_${validation_mode}.txt" + + command { + ${gatk_path} \ + ValidateSamFile \ + --INPUT ${input_bam} \ + --OUTPUT ${output_name} \ + --MODE ${default="SUMMARY" validation_mode} + } + runtime { + docker: docker + memory: machine_mem_gb + " GB" + } + output { + File validation_report = "${output_name}" + } +} \ No newline at end of file diff --git a/examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bams.input.json b/examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bams.input.json new file mode 100644 index 00000000..4dbb9708 --- /dev/null +++ b/examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bams.input.json @@ -0,0 +1,6 @@ +{ + "ValidateBamsWf.bam_array": [ + "s3://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_small.hg38.bam", + "s3://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_med.hg38.bam" + ] +} \ No newline at end of file diff --git a/packages/cdk/package-lock.json b/packages/cdk/package-lock.json index 8944fe70..27e64f67 100644 --- a/packages/cdk/package-lock.json +++ b/packages/cdk/package-lock.json @@ -1,8 +1,11281 @@ { "name": "cdk", "version": "0.1.0", - "lockfileVersion": 1, + "lockfileVersion": 2, "requires": true, + "packages": { + "": { + "name": "cdk", + "version": "0.1.0", + "dependencies": { + "constructs": "^3.3.155", + "monocdk": "^1.124.0" + }, + "devDependencies": { + "@types/jest": "^26.0.10", + "@types/node": "^10.17.27", + "@typescript-eslint/eslint-plugin": "^4.26.1", + "@typescript-eslint/parser": "^4.33.0", + "aws-cdk": "^1.124.0", + "eslint": "^7.28.0", + "eslint-config-prettier": "^8.3.0", + "eslint-plugin-import": "^2.25.2", + "eslint-plugin-prettier": "^3.4.0", + "jest": "^26.4.2", + 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engines/cromwell.md b/site/content/en/docs/Workflow engines/cromwell.md index b3147b92..96e818f0 100644 --- a/site/content/en/docs/Workflow engines/cromwell.md +++ b/site/content/en/docs/Workflow engines/cromwell.md @@ -2,6 +2,7 @@ title: "Cromwell" date: 2021-10-01T17:27:21-04:00 draft: false +weight: 20 description: > Details on the Cromwell engine deployed by Amazon Genomics CLI --- diff --git a/site/content/en/docs/Workflow engines/miniwdl.md b/site/content/en/docs/Workflow engines/miniwdl.md new file mode 100644 index 00000000..196721b1 --- /dev/null +++ b/site/content/en/docs/Workflow engines/miniwdl.md @@ -0,0 +1,75 @@ +--- +title: "miniwdl" +date: 2021-10-01T17:27:31-04:00 +draft: false +weight: 30 +description: > + Details on the miniwdl engine deployed by Amazon Genomics CLI +--- + +## Description + +[miniwdl](https://miniwdl.readthedocs.io/en/latest/index.html) is free open source software distributed under the MIT licence +developed by the [Chan Zuckerberg Initiative](https://chanzuckerberg.com/). + +The source code for miniwdl is available on [GitHub](/~https://github.com/chanzuckerberg/miniwdl). When deployed with +Amazon Genomics CLI miniwdl makes use of the [miniwdl-aws extension](/~https://github.com/miniwdl-ext/miniwdl-aws) which is +also distributed under the MIT licence. + +## Architecture + +There are four components of a miniwdl engine as deployed in an Amazon Genomics CLI context: + +### WES Adapter + +Amazon Genomics CLI communicates with the miniwdl engine via a GA4GH [WES](/~https://github.com/ga4gh/workflow-execution-service-schemas) REST service. The WES Adapter implements +the WES standard and translates WES calls into calls to the miniwdl head process. + +### Engine Batch Job + +For every workflow submitted, the WES adapter will create a new AWS Batch Job that contains the miniwdl process responsible +for running that workflow. These miniwdl "head" jobs are run in an "On-demand" AWS Fargate compute environment even when the actual workflow +tasks run in a Spot environment. This is to prevent Spot interruptions from terminating the workflow coordinator. + +### Compute Environment + +Workflow tasks are submitted by the miniwdl head job to an AWS Batch queue and run in containers using an AWS Compute Environment. +Container characteristics are defined by the resources requested in the workflow configuration. AWS Batch coordinates the elastic provisioning of EC2 instances (container hosts) +based on the available work in the queue. Batch will place containers on container hosts as space allows. + +#### EFS scratch space and S3 localization + +Any context with a miniwdl engine will use an Amazon Elastic File System (EFS) volume as scratch space. Inputs from S3 are +localized to the volume by jobs that the miniwdl engine spawns to copy these files to the volume. Outputs are copied back +to S3 using a similar process. Workflow tasks access the EFS volume to obtain inputs and write intermediates and outputs. + +The EFS volume is used by all miniwdl engine "head" jobs to store metadata necessary for call caching. + +The EFS volume will remain in your account for the lifetime of the context and are destroyed when contexts are destroyed. +Because the volume will grow in size as you run more workflows we recommend destroying the context when done to avoid on going EFS +charges. + +## Using miniwdl as a Context Engine + +You may declare miniwdl to be the `engine` for any contexts `wdl` type engine. For example: + +```yaml +contexts: + onDemandCtx: + requestSpotInstances: false + engines: + - type: wdl + engine: miniwdl +``` + +## Call Caching + +Call caching is enabled by default for miniwdl and because the metadata is stored in the contexts EFS volume call caching +will work across different engine "head" jobs. + +To disable call caching you can provide the `--no-cache` engine option. You may do this in a workflows `MANIFEST.json` by +adding the following key/ value pair. + +``` + "engineOptions": "--no-cache" +``` diff --git a/site/content/en/docs/Workflow engines/nextflow.md b/site/content/en/docs/Workflow engines/nextflow.md index e197645a..925ce0b3 100644 --- a/site/content/en/docs/Workflow engines/nextflow.md +++ b/site/content/en/docs/Workflow engines/nextflow.md @@ -2,8 +2,9 @@ title: "Nextflow" date: 2021-10-01T17:27:31-04:00 draft: false +weight: 40 description: > - Details on the Cromwell engine deployed by Amazon Genomics CLI + Details on the Nextflow engine deployed by Amazon Genomics CLI --- ## Description diff --git a/site/package-lock.json b/site/package-lock.json index 806a6104..7ecdfa78 100644 --- a/site/package-lock.json +++ b/site/package-lock.json @@ -1,8 +1,1323 @@ { "name": "tech-doc-hugo", "version": "0.0.1", - "lockfileVersion": 1, + "lockfileVersion": 2, "requires": true, + "packages": { + "": { + "name": "tech-doc-hugo", + "version": 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