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Calypso Re-Annotation Pipeline Guide

This guide provides step-by-step instructions for setting up and running the UCGD Calypso re-annotation pipeline, or to run Nextflow as needed independent of the created bash script. Each input parameter for Nextflow execution is explained in detail.

Prerequisites​

  • Access to AWS S3 buckets.
  • Access to the Mosaic server.
  • Basic understanding of genomic references (GRCh38/GRCh37).
  • Access to the EC2 environment with necessary permissions.

Step-by-Step Instructions​

If you not decide to use the given calypso.sh script here are explanations of each prompt:

1. Start the Script​

Run the script to initiate the setup.

2. Provide Required Inputs​

You will be prompted to enter the following inputs interactively:

a. VCF File Path​

  • Prompt: Enter S3 path including VCF file:
  • Description: Full S3 path where your input VCF file is located.
  • Example: s3://your-bucket/input.vcf

b. Final VCF Path​

  • Prompt: Enter S3 path for final VCF files:
  • Description: S3 path where the output/final VCF files will be stored.
  • Example: s3://your-bucket/

c. Mosaic Project ID​

  • Prompt: Enter Mosaic Project ID:
  • Description: Unique project identifier in Mosaic.
  • Example: 1685

d. Project Name​

  • Prompt: Enter Project name:
  • Description: Human-readable name for the project.
  • Example: M1685-Project

e. Mosaic Config Server​

  • Prompt: Enter Mosaic config server:
  • Description: URL or IP address of the Mosaic server configuration.
  • Example: ucgd-mosaic

f. Genomic Reference​

  • Prompt: Enter Genomic Reference to use (GRCh38/GRCh37)
  • Description: Choose the genomic reference build.
  • Options: GRCh38 or GRCh37

g. Run as Singleton​

  • Prompt: Run as singleton? (true/false)
  • Description: Indicates whether to process samples as singletons.
  • Options: true or false

Directory Setup​

  1. Work Directory

    • Path: /common/nextflow/$MOSAIC_PROJECT_ID
    • Created and permissioned the needed EFS directory for Nextflow execution.

  2. Processing Directory

    • Named: [M]$MOSAIC_PROJECT_ID
    • Contains the linked Nextflow output.

Nextflow Command Construction​

The following required parameters are assembled into a Nextflow command, but can be used to run an ad hoc process as needed:

  • --vcf: Path to input VCF.
  • --complete: Path for final VCF output.
  • --mosaic_project_id: Mosaic project identifier.
  • --mosaic_server: Mosaic server config file name.
  • --project: Project name.
  • --genome: Genomic reference (GRCh38/GRCh37).
  • -params-file: Pipeline parameters file.
  • --singleton: Whether processing as singleton.
  • -w: Work directory.
  • -profile cloud: Execute using cloud profile.
  • -with-trace: Enable tracing.
  • -resume: Resume from existing checkpoints.

Execution Confirmation​

  • Review the generated Nextflow command.
  • Confirm execution by typing yes.

If confirmed:

  • Logs into Docker.
  • Executes Nextflow pipeline.
  • Monitors execution and reports success or failure.

If not confirmed:

  • Cancels the command execution.

Important Notes​

  • Permissions: Ensure necessary AWS and EC2 permissions.
  • Storage: Validate available storage on EFS and S3.
  • Reference Genome: Consistency between input VCF and selected reference.
  • EFS: After process completion, you must remember to delete your /common/nextflow/M[project] directory, or you will incure AWS EFS charges.