Add VarDictJava somatic variant calling rule #32
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Pull Request Overview
Integrates VarDictJava somatic variant calling tool into the workflow with support for tumor/normal paired analysis and chromosome-based parallelization.
- Adds comprehensive VarDictJava rule set with chunked processing for scalability
- Includes configuration for different execution environments (local and SLURM)
- Exposes VarDictJava functionality in the main workflow
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflow/rules/vardictjava.smk | Complete VarDictJava rule implementation with variant calling, sorting, and merging |
| workflow/rules/rule_common.smk | Adds VARDICT_CHRMS configuration parsing |
| workflow/Snakefile | Includes VarDictJava rules in main workflow |
| config/day_profiles/slurm/templates/rule_config.yaml | SLURM-specific VarDictJava configuration |
| config/day_profiles/local/templates/rule_config.yaml | Local execution VarDictJava configuration |
Comments suppressed due to low confidence (1)
workflow/rules/vardictjava.smk:1
- [nitpick] Trailing commas are inconsistent - line 137 has a trailing comma after
threads: 4while line 144 has one after the conda directive. Consider removing trailing commas for consistency with other rules in the file.
import sys
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| raise Exception( | ||
| "vardict chunks can only be one contiguous range per chunk : ie: 1-4 with the non numerical chrms assigned 23=X, 24=Y,25=MT" | ||
| ) | ||
| return ret_mod_chrm(ret_str) |
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Function ret_mod_chrm is called but not defined or imported in this file, which will cause a NameError at runtime.
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| bcftools view -O b -o $bcf --threads {threads} $vcf && bcftools index --threads 4 $bcf; | ||
| done; | ||
| touch {output}; | ||
| {latency_wait}; |
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Variable latency_wait is used in shell command but not defined in params, which will cause the shell command to fail with an undefined variable error.
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| touch {output}; | ||
| {latency_wait}; | ||
| ls {output} >> {log} 2>&1; | ||
| {latency_wait}; |
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Variable latency_wait is used in shell command but not defined in params, which will cause the shell command to fail with an undefined variable error.
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| threads: 4, | ||
| resources: | ||
| vcpu=4, | ||
| threads=4, | ||
| partition=config['vardictjava']['partition'], | ||
| mem_mb=config['vardictjava']['mem_mb'], | ||
| conda: | ||
| config['vardictjava']['vardict_conda'], |
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[nitpick] Trailing commas are inconsistent - line 137 has a trailing comma after threads: 4 while line 144 has one after the conda directive. Consider removing trailing commas for consistency with other rules in the file.
| threads: 4, | |
| resources: | |
| vcpu=4, | |
| threads=4, | |
| partition=config['vardictjava']['partition'], | |
| mem_mb=config['vardictjava']['mem_mb'], | |
| conda: | |
| config['vardictjava']['vardict_conda'], | |
| threads: 4 | |
| resources: | |
| vcpu=4, | |
| threads=4, | |
| partition=config['vardictjava']['partition'], | |
| mem_mb=config['vardictjava']['mem_mb'], | |
| conda: | |
| config['vardictjava']['vardict_conda'] |
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| region=$(echo {params.cpre}{params.vchrm} | sed 's/~/\:/g' | sed 's/23\:/X\:/' | sed 's/24\:/Y\:/' | sed 's/25\:/{params.mito_code}\:/') | ||
| region=${region%:} | ||
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| mkdir -p "$(dirname {output.vcf})" | ||
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| {params.numa} vardict-java -G {params.huref} -f {params.af} -N {wildcards.sample} \ | ||
| -b "{input.tumor_cram}|{input.normal_cram}" -c 1 -S 2 -E 3 -g 4 "$region" \ |
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[P1] Build VarDict regions correctly for interval chunks
The shell command derives the region with region=$(echo {params.cpre}{params.vchrm} | sed 's/~/\:/g' ...) and passes it straight to vardict-java as "$region". When vardictchrm contains an interval such as 1~100000~200000, the sed pipeline emits chr1:100000:200000. VarDict expects the chr:start-end syntax, so the second delimiter must be converted to a hyphen before the call. As written, any attempt to use coordinate chunking will cause the rule to fail with an invalid region string. Consider mirroring the colon-to-dash handling used in other callers before invoking VarDict.
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Summary
Testing
snakemake --lint(fails: command not found)pip install snakemake(fails: Could not find a version that satisfies the requirement snakemake)pytesthttps://chatgpt.com/codex/tasks/task_e_68bf7506e95c833192fd54c0ffd456bd