This repository provides implementations of genomics workflows using Hail Batch, specifically:

• WES/WGS Seqr Loader: FASTQ -> CRAM -> GVCF -> pVCF -> Matrix Table -> Elasticsearch index, with an ability to use parts of this pipeline as e.g. a single-sample germline variant calling workflow (FASTQ -> GVCF), joint-calling pipeline (GVCF -> pVCF), AS-VQSR pipeline, etc.
• WES/WGS Large Cohort Workflow: FASTQ -> CRAM -> GVCF -> VDS with Hail Table annotations.
• GATK-SV: CRAM -> VCF and more, orchestrates GATK-SV WDL workflows in Hail Batch. See This README for more information.

Requirements:

• Analysis runner

Clone the repository recursively and change into the repository folder:

git clone --recurse-submodules [email protected]:populationgenomics/production-pipelines.git
cd production-pipelines

Seqr Loader is a combination of the following WARP-inspired workflows:

• Single-sample whole genome and WES germline calling, FASTQ -> GVCF (BWA/DRAGMAP, GATK4 HaplotypeCaller)
• Single-sample calling with re-alignment, CRAM -> GVCF (we use BAZAM to extract FASTQ from CRAM/BAM)
• Whole genome and WES joint-calling, GVCFs -> pVCF
• WES AS-VQSR and WGS VQSR workflows

As well as:

• The Broad's seqr loading pipelines
• Somalier pedigree checks
• MultiQC QC reporting.

The workflow uses Metamist as a source of FASTQ, CRAMs, and sample/participant metadata, and TOML configs for extended configuration (dataset and sequencing groups, Hail Batch parameters, Elasticsearch credentials, QC thresholds).

To run the Seqr Loader workflow on the dataset called validation, create a config file ~/myconfig.toml as follows:

[workflow]
input_datasets = ['validation']
sequencing_type = 'genome'
create_es_index_for_datasets = ['validation']
skip_sgs = [
    'CPGXXXX',  # eg: low coverage (8x)
]

Submit main.py seqr_loader to the analysis runner, and pass along the config above, as well as the cpg_workflows Docker image:

analysis-runner \
  --dataset seqr --description "Seqr Loader" --output-dir "seqr-loader" \
  --access-level standard \
  --config ~/myconfig.toml \
  --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:1.2.3 \
  main.py \
  seqr_loader

Note that you can pass multiple configs to the analysis runner, by repeating the --config option multiple times. All config will be merged by the analysis runner. For more info about configs, see team-docs.

For more options available for seqr-loader configuration, check the seqr-loader defaults in configs/defaults/seqr_loader.toml as well as cpg-workflows defaults in cpg_workflows/defaults.toml.

configs/seqr-main.toml provides relevant configuration defaults for a CPG production seqr-loader run. Specifically, in contains the list of datasets to query from Metamist and joint-call together, and a list of blacklisted sequencing groups in those datasets. Another handy configs, configs/genome.toml or configs/exome.toml, can be passed to subset sequencing groups to WGS or WES specifically. To use along with configs/seqr-main.toml, of these two must be provided, as the seqr-loader can work on only one type of data at a time.

For example, to load the genome data:

analysis-runner \
  --dataset seqr --description "Seqr Loader" --output-dir "seqr-loader" \
  --access-level full \
  --config configs/seqr-main.toml \
  --config configs/genome.toml \
  --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:latest \
  main.py \
  seqr_loader

Seqr Loader can be used partially, controlled by workflows/first_stages, workflows/last_stages, and workflows/only_stages parameters.

In order to align data, you only need to trigger the Align stage from the workflow (or CramMultiQC, if you also want a dataset-level MultiQC report), which can be done with workflows/last_stages. So you can create a configuration file like the following:

[workflow]
last_stages = ['CramMultiQC']

And assuming it's named ~/myconfig.toml, run:

analysis-runner \
  --dataset seqr --description "CRAM MultiQC" --output-dir "seqr" \
  --access-level full \
  --config configs/seqr-main.toml \
  --config configs/genome.toml \
  --config ~/myconfig.toml \
  --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:latest \
  main.py \
  seqr_loader

For exomes, replace configs/genome.toml with configs/exome.toml, or set sequencing_type = 'exome' in the workflow section.

The section workflows/input_datasets in configs/seqr-main.toml specified the list of all projects to be processed, excluding sequencing groups specified in the workflows/skip_sgs section.

QC reports for each dataset would be exposed on a web server, e.g. for validation genomes, the URL would be https://main-web.populationgenomics.org.au/validation/qc/cram/multiqc.html, and for exomes, it will be https://main-web.populationgenomics.org.au/validation/exome/qc/cram/multiqc.html.

If samples had pedigree data, a Somalier report will be run to infer and validate participant relationships, with report produced as https://main-web.populationgenomics.org.au/validation/qc/cram/somalier.html

Run the same command as in the above section, but with the following section in ~/myconfig.toml:

[workflow]
last_stages = ['GvcfMultiQC']

The genome GVCF QC report will be exposed as https://main-web.populationgenomics.org.au/validation/qc/gvcf/multiqc.html, for validation samples it would include a hap.py section with validation stats.

If you want the workflow to create Elasticsearch indices in the end, make sure you include the stage MtToEs into the workflow (if every prerequisite stage is already finished, you can specify it under first_stages), and set the workflow/create_es_index_for_datasets section with the list of datasets for which you want the indices to be created:

[workflow]
first_stages = ['MtToEs']
create_es_index_for_datasets = ['validation']

The resulting index will be named using the current datestamp, or using workflow/output_version option if it's specified. The Elasticsearch server is configured using the elasticsearch section in configs/defailts/seqr_loader.toml. The reason for not automatically creating indices for every project is that the Elasticsearch instance can easily run out of disk space, so additional safeguard is handy.

Another workflow in this repository is Hail Query workflow for large germline genomic variant calling cohorts.

Large-cohort workflow diverges from seqr-loader after the single-sample Genotype stage (which outputs GVCF files). Instead of using GATK for joint genotyping, it uses Hail VCF combiner:

1. Combine GVCFs (generated by GATK4) into a VDS format.
2. Perform sample-level QC, including, pedigree, sex and ancestry inference.
3. Perform variant-level QC, including allele-specific VQSR.

Given the config ~/myconfig.toml is:

[workflow]
input_datasets = ['validation']
sequencing_type = 'genome'
scatter_count = 20
output_version = '0.1'

Run the analysis runner:

analysis-runner \
  --dataset fewgenomes --description "Larcoh validation" --output-dir "larcoh" \
  --access-level main \
  --config ~/myconfig.toml \
  --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:latest \
  main.py \
  large_cohort

The workflow will find inputs using Metamist along with available sample metadata (e.g. known population labels, pedigree), align and call GVCFs, and follow with the VCF combiner and downstream annotation, writing the results into the gs://cpg-validation-main bucket.

Note that you can pass multiple configs to the analysis runner, by repeating the --config option multiple times. All config will be merged by the analysis runner. For more info about configs, see team-docs.

For more options available for the large-cohort workflow configuration, check the defaults in configs/defaults/large_cohort.toml, as well as cpg-workflows defaults in cpg_workflows/defaults.toml.

GVCFs are combined into a VDS folder format which is writen to gs://cpg-fewgenomes-test/vds/v0-1.vds.

• Sample-level metadata and QC is written to gs://cpg-fewgenomes-test/large-cohort/v0-1/sample_qc.ht, with the following row fields.

Metamist metadata:

's': str
'external_id': str
'dataset': str
'gvcf': str
'sex': str
'continental_pop': str
'subcontinental_pop': str

hl.sample_qc annotations:

'sample_qc': struct {
    n_het: int64,
    n_hom_var: int64,
    n_non_ref: int64,
    n_singleton: int64,
    n_singleton_ti: int64,
    n_singleton_tv: int64,
    n_snp: int64,
    n_insertion: int64,
    n_deletion: int64,
    n_transition: int64,
    n_transversion: int64,
    n_star: int64,
    r_ti_tv: float64,
    r_ti_tv_singleton: float64,
    r_het_hom_var: float64,
    r_insertion_deletion: float64,
    bases_over_gq_threshold: tuple (
        int64,
        int64,
        int64
    ),
    bases_over_dp_threshold: tuple (
        int64,
        int64,
        int64,
        int64,
        int64
    )
}

Sex imputation:

'is_female': bool
'var_data_chr20_mean_dp': float64
'chrX_mean_dp': float64
'chrX_ploidy': float64
'chrY_mean_dp': float64
'chrY_ploidy': float64
'X_karyotype': str
'Y_karyotype': str
'sex_karyotype': str
'impute_sex_stats': struct {
    f_stat: float64,
    n_called: int64,
    expected_homs: float64,
    observed_homs: int64
}

Soft filters are assigned based on the sample QC (low_coverage and bad_sample_qc_metrics) and sex imputation results (sex_aneuploidy and ambiguous_sex):

'filters': set<str>

Thresholds for sample QC filters are pulled from the config TOML (you can see the default values in configs/defaults/large_cohort.toml.

PC-Relate method is used to identify pairs of the 1st and the 2nd degree relatives (kin coefficient threshold - below which samples are considered unrelated - is specified as large_cohort.max_kin in TOML). Pairwise sample relatedness matrix is written as a Hail table index by a tuple of sample IDs: gs://cpg-fewgenomes-test/large-cohort/v0-1/relatedness.ht

Row fields:
    'i': str
    'j': str
    'kin': float64
    'ibd0': float64
    'ibd1': float64
    'ibd2': float64
----------------------------------------
Key: ['i', 'j']

gs://cpg-fewgenomes-test/large-cohort/v0-1/relateds_to_drop.ht is a sample-level table which contains related samples to drop, with top ranking sample selected from each family. Sets of unrelated individuals are determined using Hail's maximal_independent_set.

Row fields:
    's': str
    'rank': int64
----------------------------------------
Key: ['s']

PCA results are written into gs://cpg-fewgenomes-test/large-cohort/v0-1/ancestry:

• gs://cpg-fewgenomes-test/large-cohort/v0-1/ancestry/eigenvalues.ht
• gs://cpg-fewgenomes-test/large-cohort/v0-1/ancestry/loadings.ht
• gs://cpg-fewgenomes-test/large-cohort/v0-1/ancestry/scores.ht

When there are samples with known continental population available (the metamist participant metadata field with that data can be specified in the TOML as large_cohort.training_pop), a random forest method is used to infer population labels from the PCA results. The method is trained using 16 principal components as features on samples with known ancestry (the number of components can be adjusted in the TOML as well as large_cohort.n_pcs). Ancestry was assigned to all samples for which the probability of that ancestry was high enough (the threshold is configured as large_cohort.min_pop_prob in the TOML). Results are written as sample-level table gs://cpg-fewgenomes-test/large-cohort/v0-1/ancestry/inferred_pop.ht.

Row fields:
    's': str
    'scores': array<float64>
    'pop': str
    'is_training': bool
    'pca_scores': array<float64>
----------------------------------------
Key: ['s']

Plots for PCA and loadings are written to gs://cpg-fewgenomes-test-web/large-cohort/v0-1/ancestry/*, a bucket that is exposed as https://test-web.populationgenomics.org.au/fewgenomes/large-cohort/ancestry/*

For PCA and PC-relate, a dense subset of the original dataset is used. The markers for the subset are read from the references.gnomad.predetermined_qc_variants Hail table specified in the TOML config. The table is suitable for both exomes and genomes, so that a mixture of different sequencing types can be processed together. The resulting subset is written to gs://cpg-fewgenomes-test/large-cohort/v0-1/dense-subset.mt.

Variants from good quality samples are filtered using the AS-VQSR method:

1. Variants are exported into a sites-only VCF,

2. Batch jobs are submitted to create SNP and indel recalibration models using the allele-specific version of GATK Variant Quality Score Recalibration VQSR, with the standard GATK training resources (HapMap, Omni, 1000 Genomes, Mills indels), and the following features:

   • SNVs: AS_FS, AS_SOR, AS_ReadPosRankSum, AS_MQRankSum, AS_QD, AS_MQ,
   • Indels: AS_FS, AS_SOR, AS_ReadPosRankSum, AS_MQRankSum, AS_QD.

3. The models are applied to the VCFs and combine them back into one VCF.

4. VCF is converted back into a sites-only locus-level Hail table gs://cpg-fewgenomes-test/large-cohort/v0-1/vqsr.ht, with split multiallelics.

Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'filters': set<str>
    'info': struct {
        NEGATIVE_TRAIN_SITE: bool,
        POSITIVE_TRAIN_SITE: bool,
        culprit: str
    }
    'a_index': int32
    'was_split': bool

Note that the info.AS-* annotations used for AS-VQSR are dropped, and only the resulting filter label is appended into the filters field, e.g. VQSRTrancheINDEL99.50to99.90, VQSRTrancheSNP99.00to99.90 , etc. The AS_VQSLOD thresholds for assigning filters are configurable in the TOML as vqsr.snp_filter_level and vqsr.indel_filter_level.

This pipeline is largely compiled from the following two WDL workflows:

1. hail-ukbb-200k-callset/GenotypeAndFilter.AS.wdl

2. The Broad VQSR workflow documented here, translated from WDL with a help of Janis.

Frequencies are calculated using the Hail's hl.variant_qc method from good quality samples, and written to gs://cpg-fewgenomes-test/large-cohort/v0-1/frequencies.ht locus-level table with split multiallelics:

Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'a_index': int32
    'was_split': bool
    'InbreedingCoeff': float64
    'dp_stats': struct {
        mean: float64,
        stdev: float64,
        min: float64,
        max: float64
    }
    'gq_stats': struct {
        mean: float64,
        stdev: float64,
        min: float64,
        max: float64
    }
    'AC': array<int32>
    'AF': array<float64>
    'AN': int32
    'homozygote_count': array<int32>
    'call_rate': float64
    'n_called': int64
    'n_not_called': int64
    'n_filtered': int64
    'n_het': int64
    'n_non_ref': int64
    'het_freq_hwe': float64
    'p_value_hwe': float64
    'p_value_excess_het': float64
----------------------------------------
Key: ['locus', 'alleles']

Tables generated by the workflow can be applied to a VDS or a split dense matrix table in the following way:

import hail as hl

vds = hl.vds.read_vds('gs://cpg-fewgenomes-test/vds/v0-1.vds')
sample_qc_ht = hl.read_table('gs://cpg-fewgenomes-test/large-cohort/v0-1/sample_qc.ht')
relateds_to_drop_ht = hl.read_table('gs://cpg-fewgenomes-test/large-cohort/v0-1/relateds_to_drop.ht')
pop_ht = hl.read_table('gs://cpg-fewgenomes-test/large-cohort/v0-1/ancestry/inferred_pop.ht')
vqsr_ht = hl.read_table('gs://cpg-fewgenomes-test/large-cohort/v0-1/vqsr.ht')
freq_ht = hl.read_table('gs://cpg-fewgenomes-test/large-cohort/v0-1/frequencies.ht')

# Row-level tables require a split dense matrix table:
vds = hl.vds.split_multi(vds, filter_changed_loci=True)
mt = hl.vds.to_dense_mt(vds)

# Hard-filtering samples and variants:
mt = mt.filter_cols(hl.len(sample_qc_ht[mt.col_key].filters) > 0, keep=False)
mt = mt.filter_cols(hl.is_defined(relateds_to_drop_ht[mt.col_key]), keep=False)
mt = mt.filter_rows(hl.len(vqsr_ht[mt.row_key].filters) > 0, keep=False)

# Annotating samples and variants:
mt = mt.annotate_cols(**sample_qc_ht[mt.col_key])
mt = mt.annotate_cols(**pop_ht[mt.col_key])
mt = mt.annotate_rows(**vqsr_ht[mt.row_key])
mt = mt.annotate_rows(**freq_ht[mt.row_key])

The workflow is largely inspired by the Hail pipeline used for the QC of gnomAD releases. Good summaries of gnomAD QC can be found in gnomAD update blog posts:

• https://macarthurlab.org/2017/02/27/the-genome-aggregation-database-gnomad
• https://macarthurlab.org/2018/10/17/gnomad-v2-1
• https://macarthurlab.org/2019/10/16/gnomad-v3-0
• https://gnomad.broadinstitute.org/blog/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/#sample-and-variant-quality-control
• https://blog.hail.is/whole-exome-and-whole-genome-sequencing-recommendations/

Broad's GATK-SV workflow is WIP, but it can be already used to call SV evidence from individual samples.

Under the hood, the workflow invokes the GATK-SV WDL workflow using a managed Cromwell instance via the analysis runner helper functions. The WDL workflow repository is forked, and the latest commit to use is specified in gatk_sv/gatk_sv.py as a GATK_SV_COMMIT constant.

Running the workflow requires the Broad reference data copied to a workflow/reference_prefix bucket, and images copied to workflow/image_registry_prefix. In order to do that, use the following scripts:

bash sync_references.sh
python sync_images.py

The latter script will print a section for the gatk-sv.toml [images] section, that you'd need to insert there to make sure the workflow points to the latest tags. Also, when updating the GATK-SV fork, double check that the [references.broad.sv.*] sections in the config are up-to-date as well, and add new missing reference files if there are any.

Assuming python3 points to python3.10, set up a virtual environment:

python3 -m pip install virtualenv
virtualenv venv
source venv/bin/activate

Install the package, and the development environment:

pip install -e .
pip install -r requirements-dev.txt

The entry point of the codebase is main.py script. It contains WORKFLOWS dictionary, which is listing all available workflows. A workflow is defined by the final stages it needs to trigger, with each stage pulling other required stages recursively following required_stages links. Those final stages are passed to the run_workflow() function, which would orchestrate stages and required inputs.

In this documentation section, we describe in more detail how exactly it's implemented.

Hail Batch is a powerful system for workflow programming and execution using cloud compute and storage. In CPG, we manage our own Hail Batch deployment, along with the analysis-runner tool that provides an approachable and secure way to submit analysis scripts to Hail Batch.

In Hail, the workflows can be described using Python, and be built to be parts of more complex applications. E.g. the analysis-runner uses Hail Batch to drive itself, and the genomic variation analysis tool called Hail Query can use Hail Batch as a backend. All that makes Hail Batch a natural choice to design genomics workflows.

Classical genomics best-practices workflow implementations like WARP and GATK-SV use WDL to be run with Cromwell or Terra. In order to integrate WDL workflows into a Hail Batch infrastructure, there are a few possible approaches.

1. Start a Cromwell instance as part of Hail Batch job script, and submit a sub-workflow inside that job,
2. Maintain a managed Cromwell instance, and wrap only workflow submissions in a Hail Batch job,
3. Fully re-engineer WDL workflows in Python and Hail Batch.

For the GATK-SV workflow, we went with the approach #2. The workflow is quite complex, it uses many layers of branching nested sub-workflows, and it implements even minor file processing commands as separate WDL tasks. We also do not intend to adjust this workflow much as of now. In order to run GATK-SV, we support a managed Cromwell instance along with a Python helper that wraps interaction with Cromwell using Hail Batch jobs, and we utilize Cromwell API along with Swagger to explore Cromwell logs.

As for the WGS/WES germline variant workflows, we re-engineered them fully in Hail Batch, largely inspired by WARP, but with significant divergence from WARP: we added dataset-specific pedigree checks and dataset-specific MultiQC reports, allele-specific VQSR for WGS, cohort annotation using Hail Query and exporting to the Elasticsearch using scripts from seqr-loading-pipelines. There are also several CPG-specific layers, like reading inputs and metadata from Metamist; reporting analysis results back to Metamist; setting global configuration with TOML; and a necessity for a more fine-grained tuning of tool's parameters and compute resources.

To facilitate re-engineering WARP workflows and creating workflows scratch, we implemented some abstractions in this module, namely a workflow "stage" with expected inputs, outputs, and dependencies, and "stage" target ("sample", "dataset", "cohort"). Unlike WDL's concept of nested sub-workflows, Hail Batch is intrinsically lower-level, naturally providing one layer of jobs, with each job corresponding to on bash script that is run on one cloud VM. That doesn't always match a higher-level task in the application domain. For example, a workflow stage called "genotype" can include multiple jobs to generate calling intervals, partition inputs, run the genotyping tool in parallel instances, gather results, perform post-processing and filtering. That "stage" would sit between an "alignment" stage and a "joint calling" stage, and a user might need to start a workflow from a specific stage, reusing pre-existing outputs; or run the pipeline only up to a specific stage. So it's helpful to abstract a set of jobs related in a domain-specific way as a stage, with an ability to restart/skip/select stages. It also turns out that GATK-SV facilitates from these abstractions too, as it consists of multiple disconnected sub-workflows of different levels.

This library provides an abstraction interface on top of Hail Batch jobs, namely a Stage abstract class, parametrised by the Target abstract class, representing what target this stage works with.

For example, a stage that performs read alignment to produce a CRAM file, would be derived from SequencingGroupStage, and be parametrised by SequencingGroup, and a stage that performs joint-calling would be derived from CohortStage, parametrised by Cohort.

Each Stage final implementation must declare paths to the outputs it would write in the expected_outputs() method. It must also define how jobs are added into Hail Batch using the queue_jobs() method.

For example, out "Align" stage that runs BWA might look like as following:

from cpg_utils import Path
from cpg_workflows.workflow import stage, SequencingGroupStage, SequencingGroup, StageInput, StageOutput
from cpg_utils.hail_batch import get_batch

@stage
class Align(SequencingGroupStage):
    def expected_outputs(self, sequencing_group: SequencingGroup) -> Path:
        return sequencing_group.make_cram_path().path

    def queue_jobs(self, sequencing_group: SequencingGroup, inputs: StageInput) -> StageOutput | None:
        j = get_batch().new_job('BWA', self.get_job_attrs(sequencing_group))
        j.command(f'bwa ... > {j.output}')
        get_batch().write_output(j.output, str(self.expected_outputs(sequencing_group)))
        # Construct StageOutput object, where we pass a path to the results,
        return self.make_outputs(sequencing_group, self.expected_outputs(sequencing_group), [j])

The queue_jobs() method is expected to return an output of type StageOutput: you can call self.make_outputs() to construct that object.

Stages can depend on each other (i.e. they form a directed acyclic graph), which is specified using a parameter required_stages to the @stage class decorator, and the inputs parameter in queue_jobs() to get the output of a previous stage. E.g. our sequencing group genotyping stage might look like this:

from cpg_utils import Path
from cpg_workflows.workflow import stage, SequencingGroupStage, SequencingGroup, StageInput, StageOutput

Align = ...


@stage(required_stages=Align)
class Genotype(SequencingGroupStage):
    def expected_outputs(self, sequencing_group: SequencingGroup) -> Path:
        return sequencing_group.make_gvcf_path().path

    def queue_jobs(self, sequencing_group: SequencingGroup, inputs: StageInput) -> StageOutput | None:
        jobs = ...
        return self.make_outputs(sequencing_group, self.expected_outputs(sequencing_group), jobs)

Stage of different levels can depend on each other, and the library will resolve that correctly. E.g. joint calling stage that takes GVCF outputs to produce a cohort-level VCF would look like this:

from cpg_utils import Path
from cpg_workflows.workflow import stage, CohortStage, Cohort, StageInput, StageOutput

Genotype = ...


@stage(required_stages=Genotype)
class JointCalling(CohortStage):
    def expected_outputs(self, cohort: Cohort) -> Path:
        return cohort.analysis_dataset.prefix() / 'joint-called.vcf.gz'

    def queue_jobs(self, cohort: Cohort, inputs: StageInput) -> StageOutput | None:
        # Get outputs from previous stage. Because the Genotype stage
        # acts on a sequencing_group, we use a method `as_path_by_target` that returns
        # a dictionary index by sequencing group ID:
        gvcf_path_by_sg = inputs.as_path_by_target(Genotype)
        assert len(gvcf_path_by_sg) == len(cohort.get_sequencing_groups())
        jobs = ...
        return self.make_outputs(cohort, self.expected_outputs(cohort), jobs)

To submit a set of defined stages to Hail Batch, just call the run_workflow(stages) method:

from cpg_workflows.workflow import run_workflow
JointCalling = ...
run_workflow().run(stages=[JointCalling])

It takes a list of stage classes as a single parameter, and it would resolve all implicit dependencies automatically.

The library implicitly reads configuration using the cpg_utils.config.get_config() from a TOML file specified in the CPG_CONFIG_PATH environment variables, which are passed via the analysis runner's --config flag. For example, you can prepare a TOML config file config.toml as follows:

[workflow]
sequencing_type = 'genome'
only_datasets = ['hgdp', 'thousand-genomes']
skip_sgs = ['CPGXXXX', 'CPGXXXX']
skip_stages = ['Align']
check_inputs = true  # checks e.g. if fastq for align stage exist
check_intermediates = false  # explitic calls to can_reuse(path) will return False
check_expected_outputs = true  # if expected_outputs() exist, skip stage

And execute the workflow script main.py with the analysis-runner as follows:

analysis-runner --dataset seqr --access-level test -o test-workflow \
--config configs/config.toml main.py

The script would be able to access config parameters with

from cpg_utils.config import get_config
assert get_config()['workflow']['sequencing_type'] == 'genome'

Note that the workflow implicitly reads inputs from Metamist, and requires workflow/only_datasets and workflow/sequencing_type to be defined to pull proper inputs.

TOML files in configs/defaults and cpg_workflows/defaults.toml list possible configuration parameters for workflows, please refer to those configs for documentation.

Also keep in mind that analysis-runner would implicitly set a set of config parameters suitable specifically for the CPG infrastructure, e.g. the generated config after analysis-runner post-processing would look like this:

[workflow]
access_level = "test"
dataset_gcp_project = "validation"
dataset = "validation"

[hail]
billing_project = "validation"
pool_label = "large-cohort"

[images]
cpg_workflows = "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:1.4.1"
bcftools = "australia-southeast1-docker.pkg.dev/cpg-common/images/bcftools:1.16"
...

[references]
genome_build = "GRCh38"
vep_mount = "gs://cpg-common-main/references/vep/105.0/mount"
...

[references.broad]
dragmap_prefix = "gs://cpg-common-main/references/hg38/v0/dragen_reference"
...

[storage.default]
default = "gs://cpg-validation-main"
web = "gs://cpg-validation-main-web"
analysis = "gs://cpg-validation-main-analysis"
tmp = "gs://cpg-validation-main-tmp"
web_url = "https://main-web.populationgenomics.org.au/validation"
...

If you are not using the analysis runner, you'd have to set those generated values explicitly.

The cpg_utils.hail_batch module provides a helper function get_batch to set up Hail Batch in the CPG context, assuming hail/billing_project and hail/backend are set in config.

from cpg_utils.hail_batch import get_batch
b = get_batch(name='My batch')
j = b.new_job('My job', ...)
...

The Batch instance derives from a class extended from standard Hail Batch class, and it records stats of added jobs and prints statistics before submission, highlighting labelled jobs, e.g.:

Will submit 186 jobs:
BWA: 3 for 3 samples
Somalier extract (CRAMs): 3 for 3 samples
HaplotypeCaller: 3 for 3 samples
ReblockGVCF: 3 for 3 samples
Somalier extract (GVCFs): 3 for 3 samples
Other jobs: 171

The Batch instance also constructs the job name if the names of a sample and a dataset are provided as attributes, e.g.:

>>> j = b.new_job('My job', dict(sequencing_group='CPGXXXX', dataset='fewgenomes'))
>>> print(j.name)
fewgenomes/CPGXXXX: My job

cpg_utils.hail_batch provides a helper command to set up a command that can be used to add monitoring of disk space, or authenticate with GCP:

from cpg_utils.hail_batch import command
j = ...
j.command(command('sleep 600', monitor_space=True, setup_gcp=True))

This will wrap the command as follows:

set -o pipefail
set -ex
export GOOGLE_APPLICATION_CREDENTIALS=/gsa-key/key.json
gcloud -q auth activate-service-account --key-file=$GOOGLE_APPLICATION_CREDENTIALS

(while true; do df -h; du -sh $BATCH_TMPDIR; sleep 600; done) &

sleep 600

df -h; du -sh $BATCH_TMPDIR

workflow/check_expected_outputs = true controls whether the paths returned by expected_outputs() of each job correspond to existing objects, and would skip stages with already existing outputs.

You can also call the method cpg_workflows.utils.can_reuse(path) explicitly within the code called from queue_jobs(). workflow/check_intermediates = true controls whether can_reuse() checks the object(s), or always returns False.

workflow/check_inputs = true controls whether inputs to the first stage in the pipeline should be checked for existence, e.g. alignment inputs for an Align stage. skip_sgs_with_missing_input controls the behaviour if those inputs are missing: where skip such sequencing groups, or stop the workflow.

You can also start the pipeline from a specific stage with workflow/first_stages (it would skip all previous stages, but still check immediately required inputs for the first stage). workflow/last_stages would stop the workflow after the stages specified. workflow/only_stages would execute only stages specified, ignoring dependencies.

You can also force the pipeline to skip certain sequencing groups with workflow/skip_sgs, pick only certain sequencing groups with workflow/only_sgs, force re-processing of certain sequencing groups with workflow/force_sgs. workflow/skip_datasets and workflow/only_datasets are available, and more fine-grained combination of skip_sgs and skip_stages:

[workflow.skip_stages_for_sgs]
CramQC = ['CPGXXXX']

To see available workflow stages, explore the cpg_workflows/stages folder. A stage wrappers for Hail Batch jobs that allow to glue them together into genomics workflows. cpg_workflows also provides helper functions that create Hail Batch jobs for different domain-specific applications, e.g. alignment, deduplication, QC, variant calling, creating calling intervals, running VQSR, creating ES index, etc. Those jobs can be called from the queue_jobs method of a stage, or in isolation, as they don't need to know about the stage they are called from, but only need a Batch object.

Config's [slack] section activates QC reports to a Slack channel. For example:

[slack]
channel = 'workflows-qc'
token_secret_id = 'slack-seqr-loader-token'
token_project_id = 'seqr-308602'

Would send messages on QC completion to the workflows-qc channel, flagging failed samples.

Two scripts send Slack messages: check_multiqc.py and check_pedigree.py. Note that the MultiQC checks only work when the qc_thresholds section is also specified, for example:

[qc_thresholds.genome.min]
"MEDIAN_COVERAGE" = 10
"PCT_PF_READS_ALIGNED" = 0.80
[qc_thresholds.genome.max]
"FREEMIX" = 0.04
"PERCENT_DUPLICATION" = 25

Thresholds can be adjusted as needed, per workflow or dataset. Note that the metrics names here should match the ones in the MultiQC JSON.