├── .gitignore ├── 1_Setup_AWS_account ├── 1_Setup_AWS_Account.md ├── 2_Setup_AWS_client_tools.md ├── 3_Setup_AWS_Role-based_Security.md ├── README.md ├── images │ ├── aws-cli-example.png │ ├── aws-cli.png │ ├── aws-console.png │ ├── aws-locations.png │ └── example-image.png ├── scripts │ └── example-script.sh └── whitepapers │ ├── AWS_Security_Best_Practices.pdf │ └── AWS_Security_Checklist.pdf ├── 2_Files_&_Data ├── 1_Store_in_S3.md ├── 2_Use_public_genomic_datasets.md ├── 3_Query_files_Athena.md ├── 4_Transform_with_Glue.md ├── 5_Build_DataLake.md ├── README.md ├── images │ ├── 1000-genomes-mktplc.png │ ├── athena-lake.png │ ├── data-lake-arch.png │ ├── genomics-lake.png │ ├── iGenomes.png │ ├── modern-health-data-aws.png │ ├── s3-storage.png │ └── storage-option.png ├── scripts │ ├── example.sh │ └── genomic-data-samples │ │ ├── BAM │ │ ├── exampleBAM.bam │ │ └── exampleBAM.bam.bai │ │ ├── BED │ │ ├── AmpliSeqDnaCoordinateFileUpload.bed │ │ └── Annotations,Gene:Region Lists │ │ │ ├── Cancer_custom_annotation.txt │ │ │ ├── TSACP.txt │ │ │ └── TST15_coordinates_bed.bed │ │ ├── BZ2 │ │ └── GenomeAnalysisTK-3.7-0-gcfedb67.tar.bz2 │ │ ├── CSV-or-TXT │ │ ├── CSV-for-BigQuery-lessons │ │ │ ├── experiments.csv │ │ │ ├── expression.csv │ │ │ ├── genes.csv │ │ │ ├── gotree.csv │ │ │ └── memberships.csv │ │ ├── GPL1261_GKC_568_gs.txt │ │ └── gatk-data-sample.txt │ │ ├── FASTA │ │ ├── GenomeAnalysisTK.jar │ │ ├── exampleFASTA.dict │ │ ├── exampleFASTA.fasta │ │ └── exampleFASTA.fasta.fai │ │ ├── README.md │ │ ├── SAM │ │ ├── Galaxy41-[toy.sam].sam │ │ └── toy.sam │ │ ├── TSV │ │ ├── Breast Cancer Info.tsv │ │ └── terra_sample.tsv │ │ └── VCF │ │ ├── TST15 - HDC749 │ │ ├── Cancer_custom_annotation.txt │ │ ├── HDC749-Rep1.genome.vcf │ │ ├── HDC749-Rep6.genome.vcf │ │ ├── HDC749-Rep8.genome.vcf │ │ ├── TSACP.txt │ │ ├── TST15_coordinates_bed.txt │ │ └── TruSight_Myeloid.txt │ │ ├── TST26 - HorizonSample │ │ ├── Horizon-Rep1.genome.vcf │ │ ├── Horizon-Rep1.vcf │ │ ├── Horizon-Rep2.genome.vcf │ │ ├── Horizon-Rep2.vcf │ │ ├── Horizon-Rep3.genome.vcf │ │ └── Horizon-Rep3.vcf │ │ └── hg19_v0_Axiom_Exome_Plus.genotypes.all_populations.poly.vcf └── whitepapers │ ├── 0_wa-analytics-lens.pdf │ ├── 0a_Lakehouse-analysts.pdf │ ├── 1_data-lake-build.pdf │ ├── 2_data-lake-implent-guide.pdf │ ├── 3_lake-formation-dg.pdf │ ├── Intro-to-Athena-Slides.pdf │ └── aws-databases-sql.pdf ├── 3_VMs_&_Batch ├── 1_Select_EC2_VMs.md ├── 2_Scale_out_AWS_Batch.md ├── 3_Use_Nextflow_for_Pipelines.md ├── 3a_Use_Seqera_for_Nextflow.md ├── 4_Use_Cromwell_&_WDL_for_Pipelines.md ├── 5_Use_AWS_HealthOmics.md ├── 6_Use_Decision_Tree_for_scaling.md ├── README.md ├── images │ ├── AWS-DataPipeline.png │ ├── AWS-SQL-Query-Services.png │ ├── WDL-sections.png │ ├── batch-concepts.png │ ├── batch-ui1.png │ ├── batch-ui2.png │ ├── cromwell-others.png │ ├── cutandrun-flow-diagram-v1-0_2.png │ ├── dockstore.png │ ├── health-omics-arch.png │ ├── healthomics-ready.png │ ├── idseq-czi-aws.png │ ├── learn-wdl-playlist.png │ ├── learn-wdl.png │ ├── nextflow-docker.png │ ├── nextflow-rnaseq.png │ ├── nextflow-tower.png │ ├── nf-k8.png │ ├── nf-tower.png │ ├── omics-a.png │ ├── omics-arch.png │ ├── omics-b.png │ ├── omics-c.png │ ├── omics-concepts.png │ ├── omics-d.png │ ├── pipeline-arch.png │ ├── scaling-nf-aws.png │ ├── seq-1.png │ ├── seq-2.png │ ├── seq-3.png │ ├── seq-4.png │ ├── wdl-concepts.png │ └── wdl-cromwell.png ├── scripts │ ├── Workflow_Script_Examples │ │ ├── AWS-Batch │ │ │ └── AWS-Batch.sh │ │ ├── Cromwell-WDL │ │ │ ├── 0_helloWorld │ │ │ │ ├── hello.wdl │ │ │ │ ├── helloInput.json │ │ │ │ └── helloInput.wdl │ │ │ ├── 1_blastn │ │ │ │ ├── blast.wdl.json │ │ │ │ └── blastn.wdl │ │ │ └── 2_sam-to-bam │ │ │ │ └── samToBam.wdl │ │ ├── Galaxy-GA │ │ │ ├── 0_helloWorld │ │ │ │ └── helloWorld.ga │ │ │ ├── 1_sam-to-bam │ │ │ │ └── Galaxy-Workflow-sam-to-bam.ga │ │ │ └── 2_COVID-19 │ │ │ │ ├── AmrPlusPlus_Paired_Workflow-v9.ga │ │ │ │ └── Galaxy-Workflow-COVID-19__MCRA.ga │ │ └── Nextflow-NF │ │ │ ├── 0_helloWorld │ │ │ └── helloWorld.nf │ │ │ ├── 1_blastn │ │ │ ├── blastn.nf │ │ │ └── nextflow.config │ │ │ └── 2_bam_to_cram │ │ │ └── bam-2-cram.nf │ └── example.sh └── whitepapers │ ├── AWS_Fargate_Security_Overview_Whitepaper.pdf │ ├── genomics-data-transfer-analytics-and-machine-learning.pdf │ ├── idseq-aws.pdf │ └── nextflow-on-the-aws-cloud.pdf ├── 4_K8s_&_Docker_Containers ├── 1_Use_Containers_in_Pipelines.md ├── 2_Orchestrate_Containers_with_Kubernetes.md ├── 3_Use_Nextflow_with_Containers.md ├── README.md ├── images │ ├── biocontainers-search.png │ ├── blastn-dockerfile.png │ ├── csiro-vs-k8.png │ ├── k8-webui.png │ ├── tool-to-docker.png │ └── vms-containers.png ├── scripts │ └── example-script.sh └── whitepapers │ └── ELIXIR-Webinar-BioConda-BioContainers.pdf ├── 5_Serverless_&_ML ├── 1_Lambda │ ├── 1_Connect_with_Lambda.md │ ├── 2_Config_adv_Lambda.md │ ├── 3_Connect_with_Step_functions.md │ ├── images │ │ ├── csiro_fig2_gtscan_arch_1.png │ │ └── secondary-step-functions.png │ ├── scripts │ │ ├── athena.sh │ │ └── lambda.sh │ └── whitepapers │ │ └── serverless-applications-lens.pdf ├── 2_Machine_Learning │ ├── 0_Use_ML_APIs.md │ ├── 1_Use_Jupyter_Notebook_VM.md │ ├── 2_Use_ML_container_to_create_your_own_ML_model.md │ ├── 3_Use_ML_VM_instance_to_create_your_own_ML_model.md │ ├── Jupyter_Genomic_Examples │ │ ├── Blastn_Example.ipynb │ │ ├── GATK_IGV_Tutorial.ipynb │ │ ├── Hail_GWAS_Tutorial.ipynb │ │ └── VariantSpark_Example_HipsterIndex.ipynb │ ├── README.md │ ├── images │ │ ├── AWS ML chart.png │ │ └── comprehend.png │ ├── scripts │ │ └── SageMaker.sh │ └── whitepapers │ │ ├── Analyzing-Genomes-on-AWS-with-Weka-and-NVIDIA-Clara-Parabricks-W03EB2020102.pdf │ │ ├── benchmark-ML.pdf │ │ └── genomics-data-transfer-analytics-and-machine-learning.pdf └── README.md ├── 6_Automation ├── 0_Use_aws_genomics-cli.md ├── 1_Use_Code_Repository.md ├── 2_Use_Cloud_Formation.md ├── 3_Use_Container_Registry.md ├── 4_Monitor_with_CloudWatch.md ├── 5_Setup_CI-CD_with_CodePipeline.md ├── README.md ├── images │ ├── aws-ci-cd.png │ └── csrio-vs-emr.png ├── scripts │ ├── aws-sdk │ │ ├── requirements.txt │ │ └── s3.py │ ├── awscli-examples │ │ ├── 1_manage_S3.sh │ │ ├── 2_list_EC2.sh │ │ ├── 3_manage_RDS.sh │ │ └── 4_use_AWS_Batch.sh │ ├── cloudformation-example │ │ ├── bucket.json │ │ └── bucket.yaml │ └── terraform-example │ │ ├── bucket.tf │ │ ├── main.tf │ │ ├── run.sh │ │ ├── var.tf │ │ └── variable.tf └── whitepapers │ └── practicing-continuous-integration-continuous-delivery.pdf ├── 7_REF_Info ├── 1_FAQ.md ├── 2_BIO-FILE-TYPES.md ├── 3_BIO-TOOLS.md ├── 4_SERVICE-PATTERNS.md ├── 5_CONTRIBUTING.md ├── README.md ├── images │ ├── aws-genomics-arch.png │ ├── aws-genomics.png │ └── file-images │ │ ├── fasta.png │ │ ├── fastq.png │ │ ├── flow-cell.jpg │ │ ├── gatk-concepts.png │ │ ├── generate-BAM.png │ │ ├── genomeAD-browser.png │ │ ├── gvcf.png │ │ ├── sam-format.png │ 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