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/)
Project description
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
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
Requirements
- python3.9+
- An engine registered on Workbench
- Credentials for the relevant backend (supported backends: AWS)
Installation
python3 -m pip install hifi-solves-run-humanwgs
Tests
Note that you will need access to have active credentials for the various cloud backends to run the tests.
python3 -m unittest discover -b -s tests
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] [-f]
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.
-f, --force-rerun Force rerun samples that have previously been run
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
Example run command - AWS
# 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 "${REGION}" \
--organization "${ORGANIZATION}"
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