feat: NGS-bits SampleAncestry

[tdayris]

This PR adds a second tool from ngs-bits.

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 environment.linux-64.pin.txt and environment.yaml files for easy environment setup on Linux.
  • Added a new tool, NGS-bits SampleAncestry, to estimate sample ancestry based on genetic variants.
  • Implemented a Snakemake wrapper for executing the SampleAncestry command.
  • Created a sample VCF file for testing the ancestry estimation functionality.

• Bug Fixes

  • Enhanced test coverage with new test functions for SampleAncestry and autoindex workflows.

• Documentation

  • Added comprehensive metadata for the NGS-bits SampleAncestry tool, detailing its functionality and requirements.

[coderabbitai]

📝 Walkthrough

## Walkthrough
The changes in this pull request introduce several new files related to the `NGS-bits SampleAncestry` tool. A Conda environment specification is provided through `environment.linux-64.pin.txt` and `environment.yaml`, detailing package dependencies and channels. The `meta.yaml` file contains metadata about the tool's functionality and requirements. Additionally, a new Snakefile rule for testing and a sample VCF file for input are created, along with a wrapper script to facilitate command execution. Test functions for the workflow are also added to enhance testing coverage.

## Changes

| File Path                                         | Change Summary                                                                                       |
|---------------------------------------------------|-----------------------------------------------------------------------------------------------------|
| `bio/ngsbits/sampleancestry/environment.linux-64.pin.txt` | New file created for Conda environment specifications, listing package URLs and hashes.            |
| `bio/ngsbits/sampleancestry/environment.yaml`     | New file created specifying Conda channels and dependencies, including `ngs-bits` version `2024_11`. |
| `bio/ngsbits/sampleancestry/meta.yaml`            | New metadata file created detailing tool functionality, authorship, input/output specifications, and notes. |
| `bio/ngsbits/sampleancestry/test/Snakefile`       | New rule `test_ngsbits_sampleancestry` added for processing VCF files and generating output TSV.   |
| `bio/ngsbits/sampleancestry/test/sample.vcf`      | New VCF file created with metadata and variant entries for testing purposes.                        |
| `bio/ngsbits/sampleancestry/wrapper.py`           | New Snakemake wrapper script created for executing `SampleAncestry` command with logging and parameters. |
| `test_wrappers.py`                                | New test functions `test_ngsbits_sampleancestry` and `test_vg_autoindex_map` added for workflow validation. |

## Possibly related PRs
- **#3135**: Introduces a new `environment.linux-64.pin.txt` file for Conda, which is similar to the changes made in this PR that also introduces a new `environment.linux-64.pin.txt` for Deeptools.
- **#3162**: This PR also introduces a new `environment.linux-64.pin.txt` file for the Bwameth tool, aligning with the main PR's focus on creating a Conda environment specification.
- **#3165**: The introduction of a new `environment.linux-64.pin.txt` file for the Nanosim tool parallels the main PR's addition of a similar file.
- **#3302**: Similar to the main PR, this PR introduces a new `environment.linux-64.pin.txt` file for the vg giraffe tool, indicating a consistent approach to managing Conda environments across different projects.
- **#3372**: This PR updates the `meta.yaml` and Snakefile for the Merqury tool, reflecting ongoing enhancements in the bioinformatics toolset.
- **#3452**: The addition of a new `environment.linux-64.pin.txt` file for the vg autoindex giraffe tool aligns with the main PR's focus on creating environment specifications.
- **#3496**: The introduction of a new `environment.linux-64.pin.txt` file for the MTNucRatioCalculator tool parallels the main PR's focus on environment specifications.
- **#3497**: The addition of a new `environment.linux-64.pin.txt` file for the Sex.detERRmine tool aligns with the main PR's focus on creating environment specifications.

## Suggested reviewers
- johanneskoester

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[coderabbitai]

Actionable comments posted: 4

🧹 Outside diff range and nitpick comments (2)

bio/ngsbits/sampleancestry/test/Snakefile (1)

1-13: Add rule documentation

Consider adding a docstring to describe:

• Purpose of the rule
• Expected input format
• Output format and contents
• Parameter descriptions and valid ranges

 rule test_ngsbits_sampleancestry:
+    """
+    Analyze sample ancestry from VCF file(s) using NGS-bits SampleAncestry.
+    
+    Input:
+        VCF file(s) containing variant information
+    Output:
+        TSV file containing ancestry analysis results
+    Parameters:
+        -min_snps: Minimum number of SNPs required (default: 4)
+        -build: Reference genome build (default: hg19)
+    """
     input:

bio/ngsbits/sampleancestry/wrapper.py (1)

10-16: Consider adding input validation

While the setup is correct, consider adding validation for required Snakemake inputs before executing the shell command. This would provide clearer error messages if required files are missing.

Example validation:

# Validate required inputs
if not snakemake.input:
    raise ValueError("No input file specified")

🧰 Tools

🪛 Ruff (0.8.0)

12-12: Undefined name snakemake

(F821)

---

16-16: Undefined name snakemake

(F821)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 50980f1 and 7b57101.

📒 Files selected for processing (7)

• bio/ngsbits/sampleancestry/environment.linux-64.pin.txt (1 hunks)
• bio/ngsbits/sampleancestry/environment.yaml (1 hunks)
• bio/ngsbits/sampleancestry/meta.yaml (1 hunks)
• bio/ngsbits/sampleancestry/test/Snakefile (1 hunks)
• bio/ngsbits/sampleancestry/test/sample.vcf (1 hunks)
• bio/ngsbits/sampleancestry/wrapper.py (1 hunks)
• test_wrappers.py (2 hunks)

✅ Files skipped from review due to trivial changes (4)

• bio/ngsbits/sampleancestry/environment.linux-64.pin.txt
• bio/ngsbits/sampleancestry/environment.yaml
• bio/ngsbits/sampleancestry/meta.yaml
• bio/ngsbits/sampleancestry/test/sample.vcf

🧰 Additional context used

📓 Path-based instructions (2)

bio/ngsbits/sampleancestry/wrapper.py (2)

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.

---

Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

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.

🪛 Ruff (0.8.0)

bio/ngsbits/sampleancestry/wrapper.py

12-12: Undefined name snakemake

(F821)

---

16-16: Undefined name snakemake

(F821)

🔇 Additional comments (3)

bio/ngsbits/sampleancestry/wrapper.py (1)

1-9: LGTM! Well-documented file header

The file header contains all necessary metadata and documentation.

test_wrappers.py (2)

3575-3587: LGTM: Test function follows project standards

The test function for NGS-bits SampleAncestry is well-implemented:

• Uses consistent naming convention
• Follows the established test pattern
• Includes all required snakemake parameters
• Has appropriate output file verification

---

5963-5970: LGTM: Good test separation for VG autoindex

The split into separate test functions for giraffe and map outputs improves test granularity and maintainability.

[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

bio/ngsbits/sampleancestry/wrapper.py (1)

21-21: Consider removing the :q modifier

Since Snakemake handles input/output path validation, the :q modifier on the output path might be unnecessary.

-    " -out {snakemake.output:q}"
+    " -out {snakemake.output}"

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 4f6710b and 3175ddf.

📒 Files selected for processing (1)

• bio/ngsbits/sampleancestry/wrapper.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

bio/ngsbits/sampleancestry/wrapper.py (2)

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.

---

Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

📓 Learnings (1)

bio/ngsbits/sampleancestry/wrapper.py (2)

Learnt from: tdayris
PR: snakemake/snakemake-wrappers#3502
File: bio/ngsbits/sampleancestry/wrapper.py:18-23
Timestamp: 2024-11-26T14:59:03.678Z
Learning: In Snakemake wrapper scripts, Snakemake validates input and output paths, so explicit shell quoting is not necessary.

Learnt from: tdayris
PR: snakemake/snakemake-wrappers#3502
File: bio/ngsbits/sampleancestry/wrapper.py:1-23
Timestamp: 2024-11-26T15:01:13.202Z
Learning: The NGS-bits SampleAncestry wrapper in `bio/ngsbits/sampleancestry/` includes a test Snakefile, sample VCF files, and tests available in the `test/` directory.

🪛 Ruff (0.8.0)

bio/ngsbits/sampleancestry/wrapper.py

12-12: Undefined name snakemake

(F821)

---

16-16: Undefined name snakemake

(F821)

🔇 Additional comments (3)

bio/ngsbits/sampleancestry/wrapper.py (3)

1-9: LGTM: Well-structured file header

The file header contains all necessary metadata including encoding, purpose, and author information.

---

10-17: LGTM: Proper setup of logging and parameters

The implementation correctly:

• Sets up logging to capture stderr
• Handles optional extra parameters
• Note: The undefined 'snakemake' warnings from static analysis can be safely ignored as this is a Snakemake wrapper

🧰 Tools

🪛 Ruff (0.8.0)

12-12: Undefined name snakemake

(F821)

---

16-16: Undefined name snakemake

(F821)

---

18-23: 🛠️ Refactor suggestion

Add command availability check

Consider adding a check to verify that the SampleAncestry command is available before execution.

 from snakemake.shell import shell
+from shutil import which
+
+if which("SampleAncestry") is None:
+    raise RuntimeError(
+        "SampleAncestry command not found. Please ensure NGS-bits is installed correctly."
+    )
 
 log = snakemake.log_fmt_shell(

Likely invalid or redundant comment.