Add NeuSomatic variant calling rules #34
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Pull Request Overview
This PR adds NeuSomatic variant calling capabilities to the workflow by implementing both standalone and ensemble mode Snakemake rules. NeuSomatic is a somatic variant caller that can operate independently or as an ensemble method combining results from multiple other callers.
- Added two new Snakemake rules for NeuSomatic somatic variant calling: standalone and ensemble modes
- Exposed chromosome configuration parameters for NeuSomatic across different genome builds
- Integrated NeuSomatic rules into the main workflow and configuration templates
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| workflow/rules/rule_common.smk | Adds chromosome configuration parsing for NeuSomatic |
| workflow/rules/neusomatic.smk | Implements NeuSomatic standalone and ensemble variant calling rules |
| workflow/Snakefile | Includes the new NeuSomatic rules file in the workflow |
| config/day_profiles/slurm/templates/rule_config.yaml | Adds NeuSomatic configuration for SLURM environments |
| config/day_profiles/local/templates/rule_config.yaml | Adds NeuSomatic configuration for local environments |
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| "vardict": f"{base}/vardict/{wildcards.sample}.{wildcards.alnr}.vardict.vcf", | ||
| "varscan2": f"{base}/varscan2/{wildcards.sample}.{wildcards.alnr}.varscan2.vcf", | ||
| } | ||
| for caller in ["mutect2", "strelka2", "vardict", "varscan2"]: |
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The hardcoded list of callers is duplicated from the mapping dictionary keys. Consider extracting this to avoid duplication: for caller in mapping.keys():
| for caller in ["mutect2", "strelka2", "vardict", "varscan2"]: | |
| for caller in mapping.keys(): |
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| output: | ||
| vcf=MDIR + "{sample}/align/{alnr}/snv/neusomatic/{sample}.{alnr}.neusomatic.snv.vcf", | ||
| log: | ||
| MDIR + "{sample}/align/{alnr}/snv/neusomatic/log/{sample}.{alnr}.neusomatic.snv.log", | ||
| threads: config['neusomatic']['threads'] | ||
| container: | ||
| config['neusomatic']['container'] | ||
| resources: | ||
| vcpu=config['neusomatic']['threads'], | ||
| threads=config['neusomatic']['threads'], | ||
| partition=config['neusomatic']['partition'], | ||
| mem_mb=config['neusomatic']['mem_mb'], | ||
| params: | ||
| cluster_sample=ret_sample, | ||
| numa=config['neusomatic']['numa'], | ||
| shell: | ||
| r""" | ||
| set -euo pipefail | ||
| {params.numa} neusomatic.py call \ | ||
| --output {output.vcf} \ | ||
| --tumor {input.tumor_cram} \ | ||
| --normal {input.normal_cram} \ | ||
| --ref {input.ref_fa} \ | ||
| --threads {threads} >> {log} 2>&1 |
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[P1] Ensure output/log directories exist in neusomatic rule
The neusomatic rule writes its VCF and log under snv/neusomatic/... but never creates those directories before redirecting stdout/stderr. Snakemake does not auto-create parent directories for file outputs, so the shell command will fail with “No such file or directory” before neusomatic.py runs on a fresh sample. Other rules in this workflow explicitly mkdir -p $(dirname {output}) to avoid this. Consider creating the neusomatic and neusomatic/log directories prior to invoking the tool.
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| output: | ||
| vcf=MDIR + "{sample}/align/{alnr}/snv/neusomatic/{sample}.{alnr}.neusomatic_ensemble.snv.vcf", | ||
| log: | ||
| MDIR + "{sample}/align/{alnr}/snv/neusomatic/log/{sample}.{alnr}.neusomatic_ensemble.snv.log", | ||
| threads: config['neusomatic']['threads'] | ||
| container: | ||
| config['neusomatic']['container'] | ||
| resources: | ||
| vcpu=config['neusomatic']['threads'], | ||
| threads=config['neusomatic']['threads'], | ||
| partition=config['neusomatic']['partition'], | ||
| mem_mb=config['neusomatic']['mem_mb'], | ||
| params: | ||
| cluster_sample=ret_sample, | ||
| numa=config['neusomatic']['numa'], | ||
| caller_vcfs=lambda wildcards: " ".join(get_neusom_ensemble_callers(wildcards)), | ||
| shell: | ||
| r""" | ||
| set -euo pipefail | ||
| {params.numa} neusomatic.py ensemble \ | ||
| --output {output.vcf} \ | ||
| --tumor {input.tumor_cram} \ | ||
| --normal {input.normal_cram} \ | ||
| --ref {input.ref_fa} \ | ||
| --callers {params.caller_vcfs} \ | ||
| --threads {threads} >> {log} 2>&1 |
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[P1] Missing directory creation in neusomatic_ensemble rule
The ensemble rule also writes to snv/neusomatic/... without ensuring those directories exist. When this rule runs for the first time, the redirection >> {log} and --output {output.vcf} will fail if the directories were not created by another rule, causing the job to error out before the ensemble step starts. Add a mkdir -p for the VCF and log parent paths to prevent this runtime failure.
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Summary
Testing
pytestsnakemake --lint(fails: command not found)https://chatgpt.com/codex/tasks/task_e_68bf7826c1148331b3681b12d14ba543