feat: Varscan2 - SnpEff Meta wrapper

[tdayris]

I have been contacted about issue #275 . Varscan2 and SnpEff are compatible while calling somatic variants. No error is produced, and SNP are correctly annotated in the end.

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features

  • Introduced a structured meta-wrapper configuration for a bioinformatics pipeline detailing variant calling and annotation steps.
  • Added a new Snakefile that outlines a comprehensive workflow for genomic variant analysis, integrating multiple tools.
  • Updated the used wrappers file to include new bioinformatics tools for enhanced functionality.

• Tests

  • Added a new test function to verify the integration of VarScan2 with SnpEff for variant annotation.

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes introduce a new meta-wrapper configuration for a bioinformatics pipeline in the meta.yaml file, detailing five steps for variant calling and annotation. A new Snakefile establishes rules for genome analysis workflows, integrating tools like Samtools and SnpEff. The used_wrappers.yaml file is updated to include a section listing relevant bioinformatics tools. Additionally, a new test function is added to test_wrappers.py to validate the integration of VarScan2 with SnpEff. These updates enhance the structure and testing of the bioinformatics pipeline.

Changes

File	Change Summary
meta/bio/varscan2_snpeff/meta.yaml	Added description and authors fields; outlined five key steps for variant calling/annotation.
meta/bio/varscan2_snpeff/test/Snakefile	Introduced five rules: get_genome_fasta, samtools_mpileup, varscan2_somatic, snpeff_download, and snpeff_annotate.
meta/bio/varscan2_snpeff/used_wrappers.yaml	Added a new wrappers section listing five bioinformatics tools.
test_wrappers.py	Added a new test function test_varscan2_snpeff_meta(run) for testing the Snakemake command.

Suggested reviewers

• fgvieira

---

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📥 Commits

Reviewing files that changed from the base of the PR and between 5c41ca6 and 828d254.

📒 Files selected for processing (1)

• meta/bio/varscan2_snpeff/meta.yaml (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• meta/bio/varscan2_snpeff/meta.yaml

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[coderabbitai]

Actionable comments posted: 3

🧹 Outside diff range and nitpick comments (5)

meta/bio/varscan2_snpeff/meta.yaml (1)

1-17: Consider revising step categorization in the table

The table structure is clear and informative, but there's an inconsistency in the "Step" column:

• Steps 1-3 are labeled as "Call variants" but step 1 (genome sequence acquisition) is actually a prerequisite
• Steps 4-5 are correctly labeled as "Annotate calls"

Consider this revised categorization:

-    | Call variants  | Shell    | Acquire genome sequence                        |
+    | Preparation    | Shell    | Acquire genome sequence                        |

meta/bio/varscan2_snpeff/test/Snakefile (3)

13-25: Improve parameter naming and directory structure

The rule implementation is correct, but could be improved:

1. The extra parameter name could be more descriptive
2. Consider organizing outputs in a more structured way

     output:
-        "samtools/mpileup.gz",
+        "results/samtools/mpileup.gz",
     threads: 1
     log:
-        "logs/samtools_mpileup.log",
+        "logs/samtools/mpileup.log",
     params:
-        extra=" --count-orphans ",
+        mpileup_args=" --count-orphans ",

---

27-39: Update input path and add VCF version information

Consider the following improvements:

1. Update input path to match the suggested samtools output path
2. Add VCF version information in the filename
3. Organize outputs in a results directory

     input:
-        mpileup="samtools/mpileup.gz",
+        mpileup="results/samtools/mpileup.gz",
     output:
-        snp="varscan2/snp.vcf",
-        indel="varscan2/indel.vcf",
+        snp="results/varscan2/snp.vcf4.2",
+        indel="results/varscan2/indel.vcf4.2",

---

1-65: Consider architectural improvements for the workflow

While the workflow is well-structured, consider the following improvements:

1. Add workflow documentation as comments, including:

   • Input requirements
   • Expected output files
   • Resource requirements
   • Tool versions

2. Mark intermediate files as temporary:

     output:
-        "results/samtools/mpileup.gz",
+        temp("results/samtools/mpileup.gz"),

3. Add resource specifications for cluster execution:

# Add to each rule
    resources:
        mem_mb=4000,
        runtime=60

test_wrappers.py (1)

817-829: Add docstring to document test purpose

The test implementation follows the established patterns in the codebase and correctly tests the varscan2-snpeff meta wrapper. Consider adding a docstring to document what this test validates.

 def test_varscan2_snpeff_meta(run):
+    """Test the varscan2-snpeff meta wrapper by validating generation of an annotated VCF file."""
     run(
         "meta/bio/varscan2_snpeff",
         [
             "snakemake", 
             "--cores",
             "1",
             "--use-conda",
             "-F",
             "snpeff/annotated.vcf",
         ],
     )

📜 Review details

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Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 50980f1 and 117c632.

📒 Files selected for processing (4)

• meta/bio/varscan2_snpeff/meta.yaml (1 hunks)
• meta/bio/varscan2_snpeff/test/Snakefile (1 hunks)
• meta/bio/varscan2_snpeff/used_wrappers.yaml (1 hunks)
• test_wrappers.py (1 hunks)

✅ Files skipped from review due to trivial changes (1)

• meta/bio/varscan2_snpeff/used_wrappers.yaml

🧰 Additional context used

📓 Path-based instructions (1)

test_wrappers.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

🔇 Additional comments (1)

meta/bio/varscan2_snpeff/meta.yaml (1)

18-20: LGTM!

The authors section follows the correct YAML format and properly attributes the contribution.

[coderabbitai]

Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (1)

meta/bio/varscan2_snpeff/meta.yaml (1)

5-17: Consider improving the workflow description format and clarity.

While the table is visually clear, there are a few suggestions for improvement:

1. The "Step" column could be more specific instead of repeating "Call variants" multiple times
2. Consider using a more maintainable YAML list format instead of ASCII art table
3. The "Shell" tool reference is vague and could be more specific about the actual tool or command being used

Consider this alternative format:

steps:
  variant_calling:
    - name: "Genome Sequence Acquisition"
      tool: "wget/curl"  # or specific tool name
      purpose: "Acquire genome sequence"
    - name: "Variant Detection"
      tool: "Samtools"
      purpose: "Acquire a list of potential variants"
    - name: "Variant Calling"
      tool: "Varscan2"
      purpose: "Call variants with Varscan2"
  
  annotation:
    - name: "Database Preparation"
      tool: "SnpEff"
      purpose: "Download variants database"
    - name: "Variant Annotation"
      tool: "SnpEff"
      purpose: "Annotate variants with downloaded database"

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 117c632 and 40f846a.

📒 Files selected for processing (2)

• meta/bio/varscan2_snpeff/meta.yaml (1 hunks)
• meta/bio/varscan2_snpeff/test/Snakefile (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• meta/bio/varscan2_snpeff/test/Snakefile

🔇 Additional comments (2)

meta/bio/varscan2_snpeff/meta.yaml (2)

1-4: LGTM! Clear and well-structured header.

The name and description structure follow YAML best practices and clearly indicate the purpose of the meta-wrapper.

---

19-20: LGTM! Author information is properly formatted.

The author section follows the correct YAML list structure and matches the PR submitter.