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| ## Description | ||
| # Description | ||
| <!--- Briefly describe the changes included in this pull request and the paths to the test cases below | ||
| !--- starting with 'Closes #...' if appropriate ---> | ||
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| <!--Provide a brief summary of the PR here--> | ||
| ### Closes #... | ||
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| <!--- Please read each of the following items and confirm by replacing the [ ] with a [X] ---> | ||
| ## Checklist | ||
| ## Testing Results | ||
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| ### Formatting | ||
| ### Docker Image Testing | ||
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| - [ ] I have read the [code review guidelines](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List). | ||
| - [ ] I have tested the Docker image with the `docker run` command as described below. | ||
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| - [ ] The name of the branch is meaningful and well formatted following the [standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List), using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch]. | ||
| #### Test the Docker image with at least one sample. Verify the new Docker image works using: | ||
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| - [ ] I have set up or verified the branch protection rule following the [github standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request. | ||
| ```docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>``` | ||
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| ### File Updates | ||
| #### My command: | ||
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| - [ ] I have updated the version number/dependencies and added my name to the maintainer listing in the `Dockerfile`. | ||
| ```Provide the command you ran here``` | ||
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| - [ ] I have updated the version number/feature changes in the `README.md`. | ||
| ### Test Cases | ||
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| <!--- This acknowledgement is optional if you do not want to be listed---> | ||
| - [ ] I have updated the version number and added my name to the contributors listing in the `metadata.yaml`. | ||
| - Case 1 | ||
| - sample: <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 --> | ||
| - input csv: <!-- path/to/input.csv --> | ||
| - config: <!-- path/to/xxx.config --> | ||
| - output: <!-- path/to/output --> | ||
| - Case 2 | ||
| - sample: <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 --> | ||
| - input csv: <!-- path/to/input.csv --> | ||
| - config: <!-- path/to/xxx.config --> | ||
| - output: <!-- path/to/output --> | ||
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| # Checklist | ||
| <!--- Please read each of the following items and confirm by replacing the [ ] with a [X] ---> | ||
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| - [ ] I have added the changes included in this pull request to the `CHANGELOG.md` under the next release version or unreleased, and updated the date. | ||
| ### Formatting | ||
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| <!---If any previous versions have bugs, add "deprecated" in the version tag and list the bug in the corresponding release---> | ||
| - [ ] I have drafted the new version release with any addidtions/changes and have linked the `CHANGELOG.md` in the release. | ||
| - [ ] I have read the [code review guidelines](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3187646/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List). | ||
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| ### Docker Hub Auto Build Rules | ||
| - [ ] The name of the branch is meaningful and well formatted following the [standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List), using \[AD_username (or 5 letters of AD if AD is too long)]-\[brief_description_of_branch]. | ||
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| - [ ] I have created automated build rules following [this page](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/How+to+set+up+automated+builds+for+Docker+Hub) and I have not manually pushed this Docker image to the `blcdsdockerregistry` on [Docker Hub](https://hub.docker.com). | ||
| - [ ] I have set up or verified the branch protection rule following the [github standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request. | ||
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| ### Docker Image Testing | ||
| ### File Updates | ||
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| - [ ] I have tested the Docker image with the `docker run` command as described below. | ||
| - [ ] I have ensured that the version number update follows the [versioning standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3188472/Docker+image+versioning+standardization). | ||
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| Test the Docker image with at least one A-mini sample. Verify the new Docker image works using: | ||
| - [ ] I have updated the version number in the `Dockerfile`, `README.md` and `metadata.yaml` files. | ||
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| ```docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>``` | ||
| - [ ] I have updated the dependencies and added my name to the maintainer list in the `Dockerfile`. | ||
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| My command: | ||
| - [ ] I have updated the feature changes in the `README.md` (optional). | ||
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| ```Provide the command you ran here``` | ||
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| <!--- Copy and paste the results list below for more cases that were tested---> | ||
| <!--- If the case addresses an issue that should be closed, begin with "Closes <Issue #>"---> | ||
| ## Testing Results | ||
| - [ ] I have added the changes included in this pull request to the `CHANGELOG.md` under the next release version or unreleased, and updated the date. | ||
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| Closes #<!--Issue #--> | ||
| ### GitHub Packages Auto Build Rules | ||
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| - Case 1 | ||
| - sample: <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 --> | ||
| - input files: <!--path to input file(s) (if more than one, list in indented bullet points below this line)--> | ||
| - config: <!--path to config file--> | ||
| - output: <!--path to output directory--> | ||
| - [ ] I have not manually pushed this Docker image to the uclahs-cds container registry (`ghcr.io/uclahs-cds`) on [GitHub](https://github.com/orgs/uclahs-cds/packages). | ||
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| - [ ] **I have updated the `image_name`** in the `metadata.yaml` which is required by GitHub action to automatically build and push the image. |