hifi-solves-run-humanwgs 1.3.4

Upload required files and run [PacBio's Human WGS workflow](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL) via [DNAstack's Workbench](https://omics.ai/workbench/)

HiFi Solves Human WGS workflow runner

As part of the HiFi Solves Consortium, organizations will run their sequencing data through PacBio's Human Whole Genome Sequencing (WGS) pipeline.

This package handles uploading all required raw data to the organization's cloud, configures the required workflow metadata, and triggering a run of the HumanWGS workflow. Output files are automatically ingested into Publisher and made available on hifisolves.org.

Package information

• HumanWGS pipeline version: v1.1.0

Requirements

• python3.9+
• An engine registered on Workbench
• Credentials for the relevant backend (supported backends: AWS, Azure, GCP)

Installation

python3 -m pip install hifi-solves-run-humanwgs

Script usage

Arguments

usage: hifisolves-ingest [-h] [-v] [-s SAMPLE_INFO] [-m MOVIE_BAMS] [-c FAM_INFO] -b {AWS,GCP,AZURE} -r REGION -o ORGANIZATION [-e ENGINE] [-u] [-i] [-f]
                         [--aws-storage-capacity AWS_STORAGE_CAPACITY]

Upload genomics data and run PacBio's official Human WGS pipeline

options:
  -h, --help            show this help message and exit
  -v, --version         Program version
  -b {AWS,GCP,AZURE}, --backend {AWS,GCP,AZURE}
                        Backend where infrastructure is set up
  -r REGION, --region REGION
                        Region where infrastructure is set up
  -o ORGANIZATION, --organization ORGANIZATION
                        Organization identifier; used to infer bucket names
  -e ENGINE, --engine ENGINE
                        Engine to use to run the workflow. Defaults to the default engine set in Workbench.
  -u, --upload-only     Upload movie BAMs and generate inputs JSON only; do not submit the workflow. If set, --write-inputs-json will also be set automatically.
  -i, --write-inputs-json
                        Write inputs JSON and engine configuration to a file. Files will be named {family_id}.inputs.json, {family_id}.engine_params.json, {family_id}.run_tags.json.
  -f, --force-rerun     Force rerun samples that have previously been run
  --aws-storage-capacity AWS_STORAGE_CAPACITY
                        Storage capacity override for AWS HealthOmics backend. Defaults to total size of input BAMs across all samples * 8. Supply either the requested storage capacity in GB, or 'DYNAMIC' to set storage to dynamic.

Sample information:
  Provide either --sample-info, OR both --movie-bams and --fam-info

  -s SAMPLE_INFO, --sample-info SAMPLE_INFO
                        Path to sample info CSV or TSV. This file should have columns [family_id, sample_id, movie_bams, phenotypes, father_id, mother_id, sex]. See documentation for more information on the format of this file.
  -m MOVIE_BAMS, --movie-bams MOVIE_BAMS
                        Path to movie bams CSV or TSV. This file should have columns [sample_id, movie_bams]. Repeated rows for each sample can be added if the sample has more than one associated movie bam.
  -c FAM_INFO, --fam-info FAM_INFO
                        Path to family information. This file should have columns [family_id, sample_id, father_id, mother_id, sex [, phenotype1, phenotype2, phenotype3, ... phenotypeN]]. Any number of phenotype columns may be added after the sex column; the column names should be HPO terms, and values should be 2 for 'affected' or 1 for 'unaffected'.

Sample info file

The sample info file defines the set of samples that will be run through the workflow. The workflow can either be run on individual samples or on families (typically trios, where sequencing data exists for the mother, father, and child). One sample info file per cohort / workflow run should be generated; the workflow will be run on all samples within a single sample_info.csv file.

This information is organized into a CSV file with the following columns:

Column name	Description
family_id	Unique identifier for this family / cohort. If you are running a single sample through the workflow, this can be set to the same value as sample_id. Note that only one family_id should be set across all samples/rows; if you want to run more than one cohort, their information should be written into separate sample information files.
sample_id	Sample identifier
movie_bams†	Local path to a movie BAM file associated with this sample
phenotypes†	Human Phenotype Ontology (HPO) phenotypes associated with the cohort. If no particular phenotypes are desired, the root HPO term, "HP:0000001", can be used. Any sample with a phenotype set is assumed to be affected for that phenotype.
father_id	sample_id of the father. This field can be left blank if the sample's father is not included in the run.
mother_id	sample_id of the mother. This field can be left blank if the sample's mother is not included in the run.
sex	Set to either "MALE" or "FEMALE"

† There can be more than one movie bam or phenotype for a sample. If this is the case, a new row should be generated for each additional movie_bam and/or phenotype; family_id and sample_id must be set for these fields, but information from other fields need not be repeated.

Example sample info file

Singleton

Here we have a single sample, HG005, with two associated movie bams found at the local paths bams/HG005_1.hifi_reads.bam and bams/HG005_2.hifi_reads.bam. This sample does not have any phenotypes associated with it, so the phenotypes field is left blank; the root HPO term, "HP:0000001", will be set automatically. The sample is being run alone so father_id and mother_id are left blank. Sex information only needs to be included once and can be omitted for further rows associated with the same sample_id.

family_id,sample_id,movie_bams,phenotypes,father_id,mother_id,sex
HG005,HG005,bams/HG005_1.hifi_reads.bam,,,,MALE
HG005,HG005,bams/HG005_2.hifi_reads.bam,,,,

Trio

Here we have a trio of samples: a child (HG005), father (HG006), and mother (HG007). The mother and father samples have several associated movie_bams, so there are multiple rows for each. The child has only a single movie bam but two phenotypes, so there are two rows for the child, one for each unique phenotype.

family_id,sample_id,movie_bams,phenotypes,father_id,mother_id,sex
hg005-trio,HG005,bams/HG005_1.hifi_reads.bam,HP:0001250,HG006,HG007,MALE
hg005-trio,HG005,,HP:0001263,,,
hg005-trio,HG006,bams/HG006_1.hifi_reads.bam,,,,MALE
hg005-trio,HG006,bams/HG006_2.hifi_reads.bam,,,,
hg005-trio,HG007,bams/HG007_1.hifi_reads.bam,,,,FEMALE
hg005-trio,HG007,bams/HG007_2.hifi_reads.bam,,,,
hg005-trio,HG007,bams/HG007_3.hifi_reads.bam,,,,

Alternative to the sample info file - --movie-bams and --fam-info

Instead of providing a --sample-info file, you may choose to organize your information into two separate files: --movie-bams, and --fam-info.

Movie bams

Provided using the --movie-bams argument.

Column name	Description
sample_id	Sample identifier
movie_bams†	Local path to a movie BAM file associated with this sample

† There can be more than one movie bam for a sample. If this is the case, a new row should be generated for each additional movie_bam.

Example movie bam file

sample_id,movie_bams
HG005,bams/HG005_1.hifi_reads.bam
HG006,bams/HG006_1.hifi_reads.bam
HG006,bams/HG006_2.hifi_reads.bam
HG007,bams/HG007_1.hifi_reads.bam
HG007,bams/HG007_2.hifi_reads.bam
HG007,bams/HG007_3.hifi_reads.bam

Family information

Provided using the --fam-info argument. This file is related to PLINK's fam info format, with some modifications (namely, a header is required, and there can be multiple (or zero) phenotypes columns).

Column name	Description
family_id	Unique identifier for this family / cohort. If you are running a single sample through the workflow, this can be set to the same value as sample_id. Note that only one family_id should be set across all samples/rows; if you want to run more than one cohort, their information should be written into separate sample information files.
sample_id	Sample identifier
father_id	sample_id of the father. This field can be left blank if the sample's father is not included in the run.
mother_id	sample_id of the mother. This field can be left blank if the sample's mother is not included in the run.
sex	1=male, 2=female
Phenotype columns	Any number of phenotype columns may be added after the previous columns. A column name should be an HPO term (e.g. HP:0000001). Samples should have affected status set to 2 for affected, or 1 for unaffected.

Example fam info file

family_id,sample_id,father_id,mother_id,sex,HP:0001250,HP:0001263
hg005-trio,HG005,HG006,HG007,1,2,2
hg005-trio,HG006,,,1,1,1
hg005-trio,HG007,,,2,1,1

Running the script

By default, the script will both upload input files and trigger a run of the workflow.

To upload input files only, run using the --upload-only flag. This will write inputs, engine parameters, and tags JSON files:

• {family_id}.inputs.json
• {family_id}.engine_params.json
• {family_id}.run_tags.json

Example run command - AWS

The AWS HealthOmics backend requires storage capacity for the run to be set; this capacity includes all inputs, outputs, and intermediate workflow files that are generated during workflow execution. The script will attempt to estimate the required capacity based on the size of input files, but this value can be overridden by setting the --aws-storage-capacity flag to either:

• 'DYNAMIC': storage will scale dynamically as the workflow runs; you should theoretically not run out of storage space
• <storage_capacity_gb>: the storage capacity in GB, between 0 and 9600 (9.6 TB)

See the HealthOmics docs for more information on run storage.

# AWS credentials
export AWS_ACCESS_KEY_ID=""
export AWS_SECRET_ACCESS_KEY=""
export AWS_SESSION_TOKEN=""

AWS_REGION=""
# Used for naming upload and output buckets
ORGANIZATION=""

hifisolves-ingest \
    --sample-info sample_info.csv \
    --backend aws \
    --region "${AWS_REGION}" \
    --organization "${ORGANIZATION}"

Example run command - Azure

# Azure credentials
export AZURE_STORAGE_KEY=""

AZURE_REGION=""
# Used for naming upload and output buckets
ORGANIZATION=""

hifisolves-ingest \
    --sample-info sample_info.csv \
    --backend Azure \
    --region "${AZURE_REGION}" \
    --organization "${ORGANIZATION}"

If you have files already uploaded in the target storage account, their paths may be referenced in the format /<storage_account>/rawdata/path/to/file, where <storage_account> should be your organization name with hyphens removed, and the "storage" suffix added; e.g. for organization my-test-org, <storage_account> would be mytestorgstorage.

Example run command - GCP

# GCP credentials - GOOGLE_APPLICATION_CREDENTIALS should point towards a JSON file containing service account information
export GOOGLE_APPLICATION_CREDENTIALS=""

GCP_REGION=""
# Used for naming upload and output buckets
ORGANIZATION=""

hifisolves-ingest \
	--sample-info sample_info.csv \
	--backend gcp \
	--region "${GCP_REGION}" \
	--organization "${ORGANIZATION}"

Tests

Note that you will need access to have the active cloud-specific credentials below set for the various cloud backends to run the tests.

# Required AWS credentials
export AWS_ACCESS_KEY_ID=""
export AWS_SECRET_ACCESS_KEY=""
export AWS_SESSION_TOKEN=""

# Required Azure credentials
export AZURE_STORAGE_KEY=""

# Required GCP credentials
export GOOGLE_APPLICATION_CREDENTIALS=""

python3 -m unittest discover -b -s tests

Setting workflow version automatically using a Git hook

There are two locations where the workflow version is set manually (in constants.py and in the hifisolves_wrapper workflow itself). This may lead to issues when there is a new release and fork of the HumanWGS pipeline and these values are not adjusted accordingly. Running the below will set the path to the Git hooks directory to our custom hooks directory and run a blank git checkout command, which invokes the post-checkout hook and sets the workflow version in both of the aforementioned locations.

Note: The command will need to be run from the root of the repository (hifi-solves-run-humanwgs)

git config core.hooksPath hooks/ && git checkout