dev

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @nttg8100

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,130 @@
+# Giang Labs Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders at Giang Labs pledge to make participation
+in our community, projects, and research initiatives a harassment-free experience
+for everyone, regardless of age, body size, visible or invisible disability,
+ethnicity, sex characteristics, gender identity and expression, level of
+experience, education, socio-economic status, nationality, personal appearance,
+race, caste, color, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy collaborative environment that promotes scientific
+excellence and mutual respect.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community and advancement of scientific research
+- Acknowledging and respecting the contributions of all team members
+- Fostering open communication and collaboration across all levels
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the Giang Labs leadership team. All complaints will be reviewed and
+investigated promptly and fairly. For reporting, please contact nttg8100@gmail.com.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>, and
+customized for Giang Labs.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>.
+
+[homepage]: https://www.contributor-covenant.org

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Questions or Help
+    url: https://www.linkedin.com/company/giang-labs
+    about: For questions, check our documentation or email us at nttg800@gmail.com

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,42 @@
+---
+name: Bug report
+about: Report a problem with a module or pipeline in the WILDS WDL Library
+---
+
+## Bug Description
+
+**Which module or pipeline has the issue?**
+
+<!-- e.g., ww-bwa, ww-rnaseq-basic, etc. -->
+
+**What version are you using?**
+
+<!-- e.g., commit hash, release tag, or "latest from main" -->
+
+**What went wrong?**
+
+<!-- Describe what happened. Include error messages if you have them. -->
+
+**What did you expect to happen?**
+
+<!-- Describe what you thought should happen instead. -->
+
+## How to Reproduce
+
+**Steps to reproduce the issue:**
+
+<!--
+1. I ran this command: ...
+2. With these inputs: ...
+3. And got this error: ...
+-->
+
+**Input files/data:**
+
+<!-- Describe your input files (type, size, source). You don't need to share the actual files unless asked. -->
+
+## Additional Context
+
+**Anything else that might be helpful?**
+
+<!-- System info, screenshots, logs, etc. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,37 @@
+## Type of Change
+
+<!-- List all that apply:
+- New module
+- New pipeline
+- Bug fix
+- Documentation update
+- Other (please describe) -->
+
+## Description
+
+<!-- Describe what you changed and why -->
+
+## Related Issue
+
+<!-- If this closes an issue, use "Fixes #issue-number" -->
+<!-- If it just relates to an issue, use "Related to #issue-number" -->
+
+## Testing
+
+**How did you test these changes?**
+
+<!-- e.g., "Ran testrun.wdl with miniWDL using test data" -->
+
+**Did the tests pass?**
+
+<!-- Yes/No, and include any relevant output or errors -->
+
+## Documentation
+
+- [ ] I updated the README (if applicable)
+- [ ] I added/updated parameter descriptions in the WDL (if applicable)
+- [ ] I ran `make docs-preview` to check documentation rendering (if applicable)
+
+## Additional Context
+
+<!-- Anything else reviewers should know? -->