Add DeepSomatic

[yashpatel6]

Description

Adding DeepSomatic

Testing Results

NFTest a_mini-deepsomatic - <dev-dir>/log-nftest-20250903T004241Z.log

Checklist

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have reviewed the Nextflow pipeline standards.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have set up or verified the branch protection rule following the github standards before opening this pull request.

• I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed already, or do not wish to be listed. (This acknowledgement is optional.)

• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• I have tested the pipeline on at least one A-mini sample.

[Copilot]

Pull Request Overview

This PR adds DeepSomatic variant caller support to the pipeline-call-sSNV workflow. DeepSomatic is a somatic variant calling tool that leverages deep learning to identify mutations in tumor-normal paired samples.

• Adds DeepSomatic as a new algorithm option alongside existing tools (somaticsniper, strelka2, mutect2, muse)
• Implements complete DeepSomatic workflow with interval splitting, variant calling, and VCF processing
• Includes test configuration and resource allocations for the new tool

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
module/deepsomatic.nf	Main workflow module implementing DeepSomatic variant calling pipeline
module/deepsomatic-processes.nf	Process definitions for interval conversion and DeepSomatic execution
main.nf	Integration of DeepSomatic workflow into main pipeline
test/config/a_mini-deepsomatic.config	Test configuration for DeepSomatic algorithm
nftest.yml	Test case definition for DeepSomatic validation
config/template.config	Updated algorithm list to include deepsomatic
config/schema.yaml	Added deepsomatic to valid algorithm values
config/resources.json	Resource allocation definitions for DeepSomatic processes
config/methods.config	Updated valid algorithms list for paired samples
config/default.config	Added DeepSomatic version and Docker image configuration
CHANGELOG.md	Documentation of the new feature addition

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[github-actions]

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params","base_allocations","call_sSNV_DeepSomatic"]
+ {"cpus":"4","memory":"15 GB"}
@ ["params","base_allocations","convert_IntervalListToBed_GATK"]
+ {"cpus":"1","memory":"1 GB"}
@ ["params","retry_information","call_sSNV_DeepSomatic"]
+ {"memory":{"operand":"10 GB","strategy":"add"}}
@ ["params","retry_information","convert_IntervalListToBed_GATK"]
+ {"memory":{"operand":"2","strategy":"exponential"}}
@ ["params","deepsomatic_version"]
+ "1.9.0"
@ ["params","docker_image_deepsomatic"]
+ "google/deepsomatic:1.9.0"
@ ["process","withName:call_sSNV_DeepSomatic"]
+ {"cpus":"4","memory":{"1":"15 GB","2":"25 GB","3":"31 GB","closure":"retry_updater(15 GB, add, 10 GB, $task.attempt, memory)"}}
@ ["process","withName:convert_IntervalListToBed_GATK"]
+ {"cpus":"1","memory":{"1":"1 GB","2":"2 GB","3":"4 GB","closure":"retry_updater(1 GB, exponential, 2, $task.attempt, memory)"}}
@ ["valid_algorithms",["set"],{}]
+ "deepsomatic"

test/configtest-F32.json

@ ["params","base_allocations","call_sSNV_DeepSomatic"]
+ {"cpus":"4","memory":"20 GB"}
@ ["params","base_allocations","convert_IntervalListToBed_GATK"]
+ {"cpus":"1","memory":"1 GB"}
@ ["params","retry_information","call_sSNV_DeepSomatic"]
+ {"memory":{"operand":"10 GB","strategy":"add"}}
@ ["params","retry_information","convert_IntervalListToBed_GATK"]
+ {"memory":{"operand":"2","strategy":"exponential"}}
@ ["params","deepsomatic_version"]
+ "1.9.0"
@ ["params","docker_image_deepsomatic"]
+ "google/deepsomatic:1.9.0"
@ ["process","withName:call_sSNV_DeepSomatic"]
+ {"cpus":"4","memory":{"1":"20 GB","2":"30 GB","3":"40 GB","closure":"retry_updater(20 GB, add, 10 GB, $task.attempt, memory)"}}
@ ["process","withName:convert_IntervalListToBed_GATK"]
+ {"cpus":"1","memory":{"1":"1 GB","2":"2 GB","3":"4 GB","closure":"retry_updater(1 GB, exponential, 2, $task.attempt, memory)"}}
@ ["valid_algorithms",["set"],{}]
+ "deepsomatic"

If the above changes are surprising, stop and determine what happened.

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1. Automatically: Post a comment starting with "/fix-tests" (without the quotes) and I will update the tests for you (you must review my work afterwards).
2. Manually: Follow these steps on Confluence.

[sorelfitzgibbon]

Just a couple of comments

[wiz-inc-8da00b022c]

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[yashpatel6]

Tested with reduced scatter count of 20 and there was no difference in the runtime; I'll merge these allocations as they are and they can be fine-tuned if needed

[sorelfitzgibbon]

Tested on PCAWG SA190261, a 71x coverage tumor sample, runtime was 14h 7m. Six samples ran at a time and seem to have used all available memory, traces list ~27G. 20G was allocated.
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-deepsomatic/DO15110-noBQSR-deepsomatic/call-sSNV-8.2.0/SA190261/log-call-sSNV-8.2.0-20250903T175436Z