Update fgbio to 2.4.0

[BiocondaBot]

Update fgbio: 2.3.0 → 2.4.0

Info	Link or Description
Recipe	recipes/fgbio (click to view/edit other files)
Summary	A set of tools for working with genomic and high throughput sequencing data, including UMIs
Home	https://github.com/fulcrumgenomics/fgbio
Releases
Author	@fulcrumgenomics

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request involves an update to the meta.yaml file for the fgbio package. The primary changes include updating the version from "2.3.0" to "2.4.0". Along with this version change, the source URL has been modified to reflect the new version, directing it to the JAR file for version 2.4.0 instead of 2.3.0. Additionally, the SHA256 checksum has been updated to correspond with the new version, changing from a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69 to c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937. There are no other modifications to the structure, requirements, or commands within the meta.yaml file.

Possibly related PRs

• Update gencove to 2.23.0 #51404: Update gencove to 2.23.0 - This PR updates the version and SHA256 checksum for the gencove package, similar to the version and checksum updates in the main PR for the fgbio package.
• Update gencove to 2.23.1 #51819: Update gencove to 2.23.1 - This PR also updates the version and SHA256 checksum for the gencove package, reflecting a similar type of change as seen in the main PR.
• Update gencove to 2.24.0 #51849: Update gencove to 2.24.0 - This PR continues the pattern of updating the version and SHA256 checksum for the gencove package, aligning with the changes made in the main PR for fgbio.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 0d6951b and 742e619.

📒 Files selected for processing (1)

• recipes/fgbio/meta.yaml (1 hunks)

🧰 Additional context used

🪛 yamllint

recipes/fgbio/meta.yaml

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (3)

recipes/fgbio/meta.yaml (3)

1-1: LGTM: Version update is properly implemented

The version update to 2.4.0 is correctly defined and consistently referenced throughout the recipe via Jinja2 templating.

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

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Line range hint 11-24: Verify compatibility with existing dependencies

The package configuration remains unchanged. Please verify:

1. That the new version is compatible with the current dependency constraints
2. Whether any new features in 2.4.0 require additional test coverage

✅ Verification successful

Based on the release notes, I can generate the final response as there's enough information to verify the compatibility concerns.

Dependencies remain compatible with version 2.4.0

The changes in version 2.4.0 are minor feature additions and bug fixes that don't introduce breaking changes:

• Added lookup functionality to SequenceMetadata
• Added validation in CollectDuplexSeqMetrics
• Fixed filtering behavior in CallDuplexConsensusReads

These changes don't affect the core dependencies (OpenJDK, Python, R, ggplot2, scales) and maintain backward compatibility.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any breaking changes or new features in the release notes

# Fetch the release notes for version 2.4.0
gh release view 2.4.0 --repo fulcrumgenomics/fgbio || echo "Release notes not found"

# Check if there are any changes to the command-line interface
curl -sL "https://github.com/fulcrumgenomics/fgbio/releases/download/2.4.0/fgbio-2.4.0.jar" -o fgbio.jar
java -jar fgbio.jar 2>&1 | grep "Commands" -A 50

Length of output: 1145

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

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8-9: Verify SHA256 checksum of the JAR file

Let's verify that the SHA256 checksum matches the actual JAR file from the source URL.

---

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