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| 1 | +<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] ---> |
| 2 | +## Checklist |
| 3 | + |
| 4 | +### Formatting |
| 5 | + |
| 6 | +- [ ] 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). |
| 7 | + |
| 8 | +- [ ] 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]. |
| 9 | + |
| 10 | +- [ ] 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. |
| 11 | + |
| 12 | +### File Updates |
| 13 | + |
| 14 | +- [ ] I have ensured that the version number update follows the [versioning standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization). |
| 15 | + |
| 16 | +- [ ] I have updated the version number/dependencies and added my name to the maintainer list in the `Dockerfile`. |
| 17 | + |
| 18 | +- [ ] I have updated the version number/feature changes in the `README.md`. |
| 19 | + |
| 20 | +<!--- This acknowledgement is optional if you do not want to be listed---> |
| 21 | +- [ ] I have updated the version number and added my name to the contributors list in the `metadata.yaml`. |
| 22 | + |
| 23 | +- [ ] 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. |
| 24 | + |
| 25 | +<!---If any previous versions have bugs, add "deprecated" in the version tag and list the bug in the corresponding release---> |
| 26 | +- [ ] I have drafted the new version release with any additions/changes and have linked the `CHANGELOG.md` in the release. |
| 27 | + |
| 28 | +### Docker Hub Auto Build Rules |
| 29 | + |
| 30 | +- [ ] 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). |
| 31 | + |
| 32 | +### Docker Image Testing |
| 33 | + |
| 34 | +- [ ] I have tested the Docker image with the `docker run` command as described below. |
| 35 | + |
| 36 | +#### Test the Docker image with at least one sample. Verify the new Docker image works using: |
| 37 | + |
| 38 | +```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>``` |
| 39 | + |
| 40 | +#### My command: |
| 41 | + |
| 42 | +```Provide the command you ran here``` |
| 43 | + |
| 44 | +## Description |
| 45 | + |
| 46 | +<!--- Briefly describe the changes included in this pull request |
| 47 | + !--- starting with 'Closes #...' if approriate ---> |
| 48 | + |
| 49 | +Closes #... |
| 50 | + |
| 51 | +<!--- Fill out the results section below with the specific test(s) conducted for this docker image. |
| 52 | + !--- Add additional cases as necessary. |
| 53 | + !--- Remove irrelevant points (depending on the docker image being tested. |
| 54 | + !--- Add points as necessary to completely describe the test. ---> |
| 55 | +## Testing Results |
| 56 | + |
| 57 | +- Case 1 |
| 58 | + - sample: <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 --> |
| 59 | + - input files: <!--path to input file(s) (if more than one, list in indented bullet points below this line)--> |
| 60 | + - config: <!--path to config file--> |
| 61 | + - output: <!--path to output directory--> |
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