diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
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+# Contributing to CARLISLE
+
+## Proposing changes with issues
+
+If you want to make a change, it's a good idea to first
+[open an issue](https://code-review.tidyverse.org/issues/)
+and make sure someone from the team agrees that it’s needed.
+
+If you've decided to work on an issue,
+[assign yourself to the issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/assigning-issues-and-pull-requests-to-other-github-users#assigning-an-individual-issue-or-pull-request)
+so others will know you're working on it.
+
+## Pull request process
+
+We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+as our collaboration process.
+Follow the steps below for detailed instructions on contributing changes to
+CARLISLE.
+
+
+
+### Clone the repo
+
+If you are a member of [CCBR](https://github.com/CCBR),
+you can clone this repository to your computer or development environment.
+Otherwise, you will first need to
+[fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)
+the repo and clone your fork. You only need to do this step once.
+
+```sh
+git clone https://github.com/CCBR/CARLISLE
+```
+
+> Cloning into 'CARLISLE'...
+> remote: Enumerating objects: 1136, done.
+> remote: Counting objects: 100% (463/463), done.
+> remote: Compressing objects: 100% (357/357), done.
+> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673
+> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done.
+> Resolving deltas: 100% (530/530), done.
+
+```sh
+cd CARLISLE
+```
+
+### If this is your first time cloning the repo, you may need to install dependencies
+
+- Install snakemake and singularity or docker if needed (biowulf already has these available as modules).
+
+- Install the python dependencies with pip
+
+ ```sh
+ pip install .
+ ```
+
+ If you're developing on biowulf, you can use our shared conda environment which already has these dependencies installed
+
+ ```sh
+ . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+ conda activate py311
+ ```
+
+- Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
+ have it. Then from the repo's root directory, run
+
+ ```sh
+ pre-commit install
+ ```
+
+ This will install the repo's pre-commit hooks.
+ You'll only need to do this step the first time you clone the repo.
+
+### Create a branch
+
+Create a Git branch for your pull request (PR). Give the branch a descriptive
+name for the changes you will make, such as `iss-10` if it is for a specific
+issue.
+
+```sh
+# create a new branch and switch to it
+git branch iss-10
+git switch iss-10
+```
+
+> Switched to a new branch 'iss-10'
+
+### Make your changes
+
+Edit the code, write and run tests, and update the documentation as needed.
+
+#### test
+
+Changes to the **python package** code will also need unit tests to demonstrate
+that the changes work as intended.
+We write unit tests with pytest and store them in the `tests/` subdirectory.
+Run the tests with `python -m pytest`.
+
+If you change the **workflow**, please run the workflow with the test profile
+and make sure your new feature or bug fix works as intended.
+
+#### document
+
+If you have added a new feature or changed the API of an existing feature,
+you will likely need to update the documentation in `docs/`.
+
+### Commit and push your changes
+
+If you're not sure how often you should commit or what your commits should
+consist of, we recommend following the "atomic commits" principle where each
+commit contains one new feature, fix, or task.
+Learn more about atomic commits here:
+
+
+First, add the files that you changed to the staging area:
+
+```sh
+git add path/to/changed/files/
+```
+
+Then make the commit.
+Your commit message should follow the
+[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
+specification.
+Briefly, each commit should start with one of the approved types such as
+`feat`, `fix`, `docs`, etc. followed by a description of the commit.
+Take a look at the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/#summary)
+for more detailed information about how to write commit messages.
+
+```sh
+git commit -m 'feat: create function for awesome feature'
+```
+
+pre-commit will enforce that your commit message and the code changes are
+styled correctly and will attempt to make corrections if needed.
+
+> Check for added large files..............................................Passed
+> Fix End of Files.........................................................Passed
+> Trim Trailing Whitespace.................................................Failed
+>
+> - hook id: trailing-whitespace
+> - exit code: 1
+> - files were modified by this hook
>
+> Fixing path/to/changed/files/file.txt
>
+> codespell................................................................Passed
+> style-files..........................................(no files to check)Skipped
+> readme-rmd-rendered..................................(no files to check)Skipped
+> use-tidy-description.................................(no files to check)Skipped
+
+In the example above, one of the hooks modified a file in the proposed commit,
+so the pre-commit check failed. You can run `git diff` to see the changes that
+pre-commit made and `git status` to see which files were modified. To proceed
+with the commit, re-add the modified file(s) and re-run the commit command:
+
+```sh
+git add path/to/changed/files/file.txt
+git commit -m 'feat: create function for awesome feature'
+```
+
+This time, all the hooks either passed or were skipped
+(e.g. hooks that only run on R code will not run if no R files were
+committed).
+When the pre-commit check is successful, the usual commit success message
+will appear after the pre-commit messages showing that the commit was created.
+
+> Check for added large files..............................................Passed
+> Fix End of Files.........................................................Passed
+> Trim Trailing Whitespace.................................................Passed
+> codespell................................................................Passed
+> style-files..........................................(no files to check)Skipped
+> readme-rmd-rendered..................................(no files to check)Skipped
+> use-tidy-description.................................(no files to check)Skipped
+> Conventional Commit......................................................Passed
> [iss-10 9ff256e] feat: create function for awesome feature
+> 1 file changed, 22 insertions(+), 3 deletions(-)
+
+Finally, push your changes to GitHub:
+
+```sh
+git push
+```
+
+If this is the first time you are pushing this branch, you may have to
+explicitly set the upstream branch:
+
+```sh
+git push --set-upstream origin iss-10
+```
+
+> Enumerating objects: 7, done.
+> Counting objects: 100% (7/7), done.
+> Delta compression using up to 10 threads
+> Compressing objects: 100% (4/4), done.
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done.
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects.
+> remote:
+> remote: Create a pull request for 'iss-10' on GitHub by visiting:
+> remote: https://github.com/CCBR/CARLISLE/pull/new/iss-10
+> remote:
+> To https://github.com/CCBR/CARLISLE
>
> [new branch] iss-10 -> iss-10
+> branch 'iss-10' set up to track 'origin/iss-10'.
+
+We recommend pushing your commits often so they will be backed up on GitHub.
+You can view the files in your branch on GitHub at
+`https://github.com/CCBR/CARLISLE/tree/`
+(replace `` with the actual name of your branch).
+
+### Create the PR
+
+Once your branch is ready, create a PR on GitHub:
+
+
+Select the branch you just pushed:
+
+
+
+Edit the PR title and description.
+The title should briefly describe the change.
+Follow the comments in the template to fill out the body of the PR, and
+you can delete the comments (everything between ``) as you go.
+Be sure to fill out the checklist, checking off items as you complete them or
+striking through any irrelevant items.
+When you're ready, click 'Create pull request' to open it.
+
+
+
+Optionally, you can mark the PR as a draft if you're not yet ready for it to
+be reviewed, then change it later when you're ready.
+
+### Wait for a maintainer to review your PR
+
+We will do our best to follow the tidyverse code review principles:
+.
+The reviewer may suggest that you make changes before accepting your PR in
+order to improve the code quality or style.
+If that's the case, continue to make changes in your branch and push them to
+GitHub, and they will appear in the PR.
+
+Once the PR is approved, the maintainer will merge it and the issue(s) the PR
+links will close automatically.
+Congratulations and thank you for your contribution!
+
+### After your PR has been merged
+
+After your PR has been merged, update your local clone of the repo by
+switching to the main branch and pulling the latest changes:
+
+```sh
+git checkout main
+git pull
+```
+
+It's a good idea to run `git pull` before creating a new branch so it will
+start from the most recent commits in main.
+
+## Helpful links for more information
+
+- [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+- [semantic versioning guidelines](https://semver.org/)
+- [changelog guidelines](https://keepachangelog.com/en/1.1.0/)
+- [tidyverse code review principles](https://code-review.tidyverse.org)
+- [reproducible examples](https://www.tidyverse.org/help/#reprex)
+- [nf-core extensions for VS Code](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack)
diff --git a/docs/changelog.md b/docs/changelog.md
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+++ b/docs/changelog.md
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+--8<-- "CHANGELOG.md"
+
+
diff --git a/docs/contributing.md b/docs/contributing.md
new file mode 100644
index 0000000..773a7e5
--- /dev/null
+++ b/docs/contributing.md
@@ -0,0 +1,3 @@
+--8<-- ".github/CONTRIBUTING.md"
+
+