Github actions workflow execution

Skill HolobiomicsLab/asb-skill-collections/packs/metabolomics/ms-generic/skills/github-actions-workflow-execution

Curated, evidence-grounded skill and software-tool collections for scientific AI agents, generated by the AgenticScienceBuilder

Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill github-actions-workflow-execution

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

14 stars14 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.

What its author says it does

Copied from the file, not written here

Use when you have a GitHub repository containing scientific records (e.

The file declares its own license as CC-BY-4.0. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

6.0 KB, as published. Nobody here has run it

github-actions-workflow-execution

Summary

Execute automated validation workflows on a GitHub repository using GitHub Actions to test all records against a validator tool, generating pass/fail status reports. This skill enables continuous integration of quality control for scientific data repositories by triggering scheduled or event-driven validation jobs that persist results as machine-readable outputs and status badges.

When to use

You have a GitHub repository containing scientific records (e.g., mass spectrometry data, chemical records, genomic datasets) that require systematic validation against a schema or reference validator, and you want to automate this validation on every commit or branch update without manual intervention.

When NOT to use

Validator tool is computationally prohibitive or exceeds GitHub Actions job time/resource limits for the number of records
Records are stored outside the GitHub repository (e.g., in a separate database) and cannot be accessed by the workflow runner
Validation results must be generated interactively or require manual review steps that cannot be scripted in a workflow

Inputs

GitHub repository with scientific records (MassBank records in .txt or similar format)
Validator tool or CLI application (e.g., MassBank-web Validator class)
GitHub Actions workflow definition file (.yml in .github/workflows/)
Branch name(s) or trigger event configuration

Outputs

Validation status report (JSON or CSV format) with pass/fail outcomes per record set
GitHub Actions workflow run logs and execution summary
Validation status badge SVG/URL for embedding in README or documentation
Per-record validation result details (errors, warnings, schema violations)

How to apply

Set up a GitHub Actions workflow file (e.g., validate-records.yml) in the .github/workflows directory that invokes your validator tool (in this case, the MassBank-web Validator) against all records in the repository. Configure the workflow to run on pushes to specified branches (main, dev) or on a schedule. The workflow collects validation results for each record and record set, then outputs results in a machine-readable format (JSON or CSV). Display validation status via GitHub Actions workflow badges linked to the workflow runs page, allowing stakeholders to see pass/fail status at a glance. Monitor the workflow execution logs to debug validation failures and iterate on record corrections.

Related tools

GitHub Actions (Orchestrates workflow execution, triggers validation on branch pushes, manages job environment and logs) — https://github.com/features/actions
MassBank-web Validator (Validates content and schema compliance of all MassBank records; invoked by the workflow against each record) — https://github.com/MassBank/MassBank-web
MassBank-data repository (Source repository containing all records to be validated; hosts the workflow definition) — https://github.com/MassBank/MassBank-data

Evaluation signals

Workflow file (.github/workflows/validate-records.yml) exists and is syntactically valid YAML
Workflow execution completes without runner errors; logs show validator invocation on all records
Validation status badges display correct pass/fail state and link to corresponding branch workflow runs
Output report (JSON/CSV) contains an entry for every record in the repository; no records are skipped
Pass/fail outcomes in the report align with independent manual validation or match expected schema constraints

Limitations

GitHub Actions has job timeout limits (~6 hours) that may prevent validation of extremely large repositories
Validator tool must be accessible from the GitHub-hosted runner environment; private or non-public validators may require additional authentication setup
Workflow badge status reflects only the most recent workflow run; historical validation trends require separate archival or dashboard integration
MassBank-web repository is deprecated; new validator maintenance has moved to https://github.com/MassBank/MassBank-cli-tools

Evidence

[intro] GitHub Actions to validate the content of all records: "uses GitHub Actions to validate the content of all records with the Validator from MassBank-web"
[readme] Validation workflow and status outputs: "uses GitHub Actions to validate the content of all records with the [Validator](https://github.com/MassBank/MassBank-web/blob/main/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Validator.ja"
[readme] Status badges displayed for branches: "* main branch []"
[other] Machine-readable output format requirement: "Output the validation report in a machine-readable format (JSON or CSV)"