feat: Deeptools multibigwig summary

[tdayris]

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 new files for setting up Conda environments (environment.linux-64.pin.txt, environment.yaml) to streamline installation for DeepTools.
  • Added a meta.yaml file providing essential metadata and configuration for the deeptools multi bigwig summary tool.
  • Created a wrapper.py script to facilitate integration of the multiBigwigSummary command within Snakemake workflows.
  • Added test cases for the multibigwigsummary command to ensure functionality with different inputs.

• Documentation

  • Enhanced user guidance with new configuration files and structured metadata for better usability in genomic analyses.

• Tests

  • Included new tests for the deeptools multibigwigsummary functionality to improve coverage and reliability.

[coderabbitai]

Walkthrough

The changes introduce new configuration files for the DeepTools project, specifically for the multiBigwigSummary tool. These include an environment specification file for Conda, a metadata file outlining the tool's functionality, and testing scripts for workflow integration. Additional test data files are provided to facilitate genomic interval analysis. The modifications enhance the project's structure and usability for bioinformatics applications.

Changes

Files	Change Summary
bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt	New file created with explicit package dependencies for Conda environment setup.
bio/deeptools/multibigwigsummary/environment.yaml	New file defining environment configuration with channels and dependencies for DeepTools.
bio/deeptools/multibigwigsummary/meta.yaml	New metadata file providing tool description, inputs, outputs, and parameters for the summary.
bio/deeptools/multibigwigsummary/test/Snakefile	New file with rules for Snakemake workflow to process bigwig files.
bio/deeptools/multibigwigsummary/test/blacklist.bed	New file containing a dataset for regions to exclude in analyses.
bio/deeptools/multibigwigsummary/test/intervals.bed	New file with genomic interval definitions for analysis.
bio/deeptools/multibigwigsummary/wrapper.py	New wrapper script for integrating multiBigwigSummary command into Snakemake workflows.
test.py	New test function added to execute the multibigwigsummary command with different parameters.

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[coderabbitai]

Actionable comments posted: 2

Outside diff range, codebase verification and nitpick comments (2)

bio/deeptools/multibigwigsummary/test/Snakefile (2)

1-14: Consider using a more descriptive log file name.

The log file name bins.logs is too generic. Consider using a more descriptive name to better understand the context of the logs.

Example:

-    log:
-        "bins.logs"
+    log:
+        "logs/test_deeptools_multibwsummary_bins.log"

---

16-30: Consider using a more descriptive log file name.

The log file name bins.logs is too generic. Consider using a more descriptive name to better understand the context of the logs.

Example:

-    log:
-        "bins.logs"
+    log:
+        "logs/test_deeptools_multibwsummary_bed.log"

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between a248fa9 and 1c410c9.

Files selected for processing (8)

• bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt (1 hunks)
• bio/deeptools/multibigwigsummary/environment.yaml (1 hunks)
• bio/deeptools/multibigwigsummary/meta.yaml (1 hunks)
• bio/deeptools/multibigwigsummary/test/Snakefile (1 hunks)
• bio/deeptools/multibigwigsummary/test/blacklist.bed (1 hunks)
• bio/deeptools/multibigwigsummary/test/intervals.bed (1 hunks)
• bio/deeptools/multibigwigsummary/wrapper.py (1 hunks)
• test.py (1 hunks)

Files skipped from review due to trivial changes (3)

• bio/deeptools/multibigwigsummary/environment.yaml
• bio/deeptools/multibigwigsummary/test/blacklist.bed
• bio/deeptools/multibigwigsummary/test/intervals.bed

Additional context used

Path-based instructions (2)

bio/deeptools/multibigwigsummary/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.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

bio/deeptools/multibigwigsummary/wrapper.py

12-12: Undefined name snakemake

(F821)

---

13-13: Undefined name snakemake

(F821)

---

15-15: Undefined name snakemake

(F821)

---

19-19: Undefined name snakemake

(F821)

---

23-23: Undefined name snakemake

(F821)

Additional comments not posted (18)

bio/deeptools/multibigwigsummary/meta.yaml (8)

1-1: LGTM!

The name is correctly defined.

The code changes are approved.

---

2-2: LGTM!

The URL is correctly defined.

The code changes are approved.

---

3-4: LGTM!

The description is correctly defined.

The code changes are approved.

---

5-6: LGTM!

The author is correctly defined.

The code changes are approved.

---

7-10: LGTM!

The input section is correctly defined.

The code changes are approved.

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11-13: LGTM!

The output section is correctly defined.

The code changes are approved.

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14-15: LGTM!

The params section is correctly defined.

The code changes are approved.

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16-17: LGTM!

The notes section is correctly defined.

The code changes are approved.

bio/deeptools/multibigwigsummary/wrapper.py (7)

1-6: LGTM!

The metadata section is correctly defined.

The code changes are approved.

---

9-9: LGTM!

The import statement is correctly defined.

The code changes are approved.

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11-13: LGTM!

The optional parameters are correctly defined.

The code changes are approved.

Tools

Ruff

12-12: Undefined name snakemake

(F821)

---

13-13: Undefined name snakemake

(F821)

---

15-17: LGTM!

The blacklist parameter is correctly defined.

The code changes are approved.

Tools

Ruff

15-15: Undefined name snakemake

(F821)

---

19-21: LGTM!

The out_raw_counts parameter is correctly defined.

The code changes are approved.

Tools

Ruff

19-19: Undefined name snakemake

(F821)

---

23-27: LGTM!

The bed parameter is correctly defined.

The code changes are approved.

Tools

Ruff

23-23: Undefined name snakemake

(F821)

---

30-36: LGTM!

The shell command is correctly defined.

The code changes are approved.

bio/deeptools/multibigwigsummary/environment.linux-64.pin.txt (3)

1-3: LGTM!

The header section provides clear instructions for creating a conda environment using the file.

The code changes are approved.

---

4-4: LGTM!

The @EXPLICIT directive is correctly used to ensure reproducibility.

The code changes are approved.

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5-112: LGTM!

The list of package URLs is correctly specified to ensure the environment is created with the exact versions required.

The code changes are approved.