PD-3137 Add mitofinder to buildindices wdl

[khajoue2]

Description

Title: Run MitoFinder optionally and Record MitoFinder execution details in metadata output

This PR enhances the metadata.txt output file by adding a dedicated section that records the execution status and parameters of the optional MitoFinder step.

The primary changes include:

1. Adding a new task to run MitoFinder script from warp-tools.
2. Adding new inputs to the RecordMetadata task (was_mitofinder_run, organism, mito_accession_used, etc.) to accept information about the mitochondrial annotation step. Implementing conditional logic within the RecordMetadata task's command block. It now checks if MitoFinder was run and, if so, logs all the relevant parameters used for the run. Updating the call to RecordMetadata within the main BuildIndices workflow to pass the necessary variables down to the task.

The motivation for this change is to improve the pipeline's provenance and traceability. Previously, the output metadata did not capture whether the optional but critical run_mitofinder step was performed. This made it difficult for users to know if the final genome indices included an annotated mitochondrial sequence without manually inspecting the files. This pull request solves that problem by explicitly stating in the metadata whether the step was run and detailing the exact inputs used, thus improving the clarity and reproducibility of the workflow's results.

This change addresses the need for more comprehensive logging of optional pipeline steps.

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Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.

• Did you add inputs, outputs, or tasks to a workflow?
• Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• If you made a changelog update, did you update the pipeline version number?

[github-actions]

Remember to squash merge!

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
BuildIndices.wdl and BuildIndices.changelog.md do not have matching versions
Some WDLs or changelog files need updating. See output for details.
validation_failed

[Copilot]

Pull Request Overview

This PR adds optional MitoFinder functionality to the BuildIndices workflow, allowing users to append mitochondrial sequence and annotations to genome references for non-human/non-mouse organisms. The changes enhance metadata recording to track MitoFinder execution details and update pipeline versioning accordingly.

• Added MitoAnnotate task to run MitoFinder with configurable inputs
• Enhanced RecordMetadata task to log MitoFinder execution status and parameters
• Updated pipeline to use MitoFinder-modified files for index building when applicable

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
BuildIndices.wdl	Adds MitoAnnotate task, new workflow inputs, conditional logic for MitoFinder execution, and enhanced metadata recording
BuildIndices.changelog.md	Documents the new MitoFinder functionality in version 5.1.0
pipeline_versions.txt	Updates BuildIndices version from 4.1.0 to 5.1.0

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