chore: Merge branch 'main' into fix-cache

.github/CONTRIBUTING.md

@@ -0,0 +1,262 @@
+# Contributing to XAVIER
+
+## 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
+XAVIER.
+
+![GitHub Flow diagram](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/GitHub-Flow_bg-white.png)
+
+### 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/XAVIER
+```
+
+> Cloning into 'XAVIER'... <br>
+> remote: Enumerating objects: 1136, done. <br>
+> remote: Counting objects: 100% (463/463), done. <br>
+> remote: Compressing objects: 100% (357/357), done. <br>
+> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673 <br>
+> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done. <br>
+> Resolving deltas: 100% (530/530), done. <br>
+
+```sh
+cd XAVIER
+```
+
+### 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:
+<https://www.freshconsulting.com/insights/blog/atomic-commits/>
+
+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 <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Failed <br>
+>
+> - hook id: trailing-whitespace <br>
+> - exit code: 1 <br>
+> - files were modified by this hook <br> > <br>
+>   Fixing path/to/changed/files/file.txt <br> > <br>
+>   codespell................................................................Passed <br>
+>   style-files..........................................(no files to check)Skipped <br>
+>   readme-rmd-rendered..................................(no files to check)Skipped <br>
+>   use-tidy-description.................................(no files to check)Skipped <br>
+
+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 <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Passed <br>
+> codespell................................................................Passed <br>
+> style-files..........................................(no files to check)Skipped <br>
+> readme-rmd-rendered..................................(no files to check)Skipped <br>
+> use-tidy-description.................................(no files to check)Skipped <br>
+> Conventional Commit......................................................Passed <br> > [iss-10 9ff256e] feat: create function for awesome feature <br>
+> 1 file changed, 22 insertions(+), 3 deletions(-) <br>
+
+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. <br>
+> Counting objects: 100% (7/7), done. <br>
+> Delta compression using up to 10 threads <br>
+> Compressing objects: 100% (4/4), done. <br>
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done. <br>
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0 <br>
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects. <br>
+> remote: <br>
+> remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
+> remote: https://github.com/CCBR/XAVIER/pull/new/iss-10 <br>
+> remote: <br>
+> To https://github.com/CCBR/XAVIER <br> > <br> > [new branch] iss-10 -> iss-10 <br>
+> branch 'iss-10' set up to track 'origin/iss-10'. <br>
+
+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/XAVIER/tree/<your-branch-name>`
+(replace `<your-branch-name>` with the actual name of your branch).
+
+### Create the PR
+
+Once your branch is ready, create a PR on GitHub:
+<https://github.com/CCBR/XAVIER/pull/new/>
+
+Select the branch you just pushed:
+
+![Create a new PR from your branch](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/new-PR.png)
+
+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 `<!--` and `-->`) 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.
+
+![Open the PR after editing the title and description](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/create-PR.png)
+
+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:
+<https://code-review.tidyverse.org/>.
+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)

.github/workflows/build-docker-meta.yml

@@ -0,0 +1,46 @@
+name: build-docker-meta
+
+on:
+  workflow_dispatch:
+    inputs:
+      context_dir:
+        type: string
+        description: path to the directory containing the Dockerfile and meta.yml file (e.g. common/ccbr_chipseeker/)
+        required: true
+      push:
+        type: boolean
+        description: Push to DockerHub (uncheck to only build the container without pushing)
+        required: true
+        default: true
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/[email protected]
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/${{ github.event.inputs.context_dir }}/meta.yml
+      - name: Login to DockerHub
+        if: ${{ github.event.inputs.push == 'true' }}
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Prepare build-time variables
+        id: vars
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_OUTPUT"
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        # only try building & pushing the container if parsing the metadata worked
+        if: ${{ steps.metadata.outputs['container'] != '' }}
+        with:
+          context: ${{ github.event.inputs.context_dir }}
+          push: ${{ github.event.inputs.push }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.vars.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}

.github/workflows/docker.yml

@@ -0,0 +1,64 @@
+name: docker
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "docker/**"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "docker/**"
+  workflow_dispatch:
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix-metadata: ${{ steps.metadata.outputs.matrix }}
+    steps:
+      - uses: hellofresh/action-changed-files@v3
+        id: metadata
+        with:
+          pattern: docker/(?P<image_dir>\w+)/.*
+          default-patterns: |
+            meta.yml
+            Dockerfile
+
+  update-docker:
+    needs: [generate-matrix]
+    strategy:
+      matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
+    if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/[email protected]
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
+      - name: Get date
+        id: date
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
+      - name: Login to DockerHub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        # only try building & pushing the container if parsing the metadata worked
+        if: ${{ steps.metadata.outputs['container'] != '' }}
+        with:
+          context: docker/${{ matrix.image_dir }}
+          # only push container to docker hub if not triggered from a PR
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.date.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}

CHANGELOG.md

@@ -1,7 +1,16 @@
 ## XAVIER development version
 
+- Fix minor bug in assess_significance.R script associated with rule freec_exome_somatic (#120, @samarth8392)
 - Fix `cache` subcommand to correctly read the container images config file. (#124, @kelly-sovacool)
 
+## XAVIER 3.1.1
+
+- New contributing guide available on GitHub and the documentation website. (#114, @kelly-sovacool)
+- New `xavier debug` subcommand to determine the base directory for debugging purposes. (#114, @kelly-sovacool)
+- Upgraded `ccbr_wes_base` docker to v1.1.0 with updated GATK version to v4.6.0.0 (#116, @samarth8392)
+- Upgrade multiqc container to use v1.15. (#117, @kelly-sovacool)
+- Upgrade memory for rule "bwa_mem" to 100G (#118, @samarth8392)
+
 ## XAVIER 3.1.0
 
 ### new features

CITATION.cff

@@ -46,5 +46,5 @@ identifiers:
   - description: Archived snapshots of all versions
     type: doi
     value: 10.5281/zenodo.12727315
-version: v3.1.0
-date-released: "2024-08-27"
+version: v3.1.1
+date-released: "2024-10-02"