Merge pull request #1 from uclahs-cds/maotian-create-docker-strelka2

Create docker repo blcdsdockerregistry/strelka2:2.9.10

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,56 @@
+## Description
+
+<!--Provide a brief summary of the PR here-->
+
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
+## Checklist 
+
+### Formatting
+
+- [ ] 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).
+
+- [ ] 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].
+
+- [ ] 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.
+
+### File Updates
+
+- [ ] I have updated the version number/dependencies and added my name to the maintainer listing in the `Dockerfile`.
+
+- [ ] I have updated the version number/feature changes in the `README.md`.
+
+<!--- 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`.
+
+- [ ] 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.
+
+<!---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. 
+
+### Docker Hub Auto Build Rules
+
+- [ ] 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).
+
+### Docker Image Testing
+
+- [ ] I have tested the Docker image with the `docker run` command as described below.
+
+Test the Docker image with at least one A-mini sample. Verify the new Docker image works using:
+
+```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>```
+
+My command: 
+
+```Provide the command you ran here```
+
+<!--- 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
+
+Closes #<!--Issue #-->
+
+- 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-->

CHANGELOG.md

@@ -8,30 +8,13 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
-### Changed
-- Changed something but it is not part of the last release.
-
----
 
-## [1.0.0] - YYYY-MM-DD
 ### Added
-- For new features.
-- Added item 1.
 
 ### Changed
-- For changes in existing functionality.
-- Changed item 1.
-
-### Deprecated
-- For soon-to-be removed features.
 
-### Removed
-- For now removed features.
-- Removed item 1.
-
-### Fixed
-- For any bug fixes.
-- Fixed item 1.
+---
 
-### Security
-- In case of vulnerabilities.
+## [2.9.10] - 2021-11-01
+### Added
+- Create the docker repo: blcdsdockerregistry/strelka2:2.9.10.

Dockerfile

@@ -1,14 +1,14 @@
-FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
+FROM blcdsdockerregistry/bl-base:1.1.0 AS builder
 
 # Use conda to install tools and dependencies into /usr/local
-ARG TOOL_VERSION=X.X.X
-RUN conda create -qy -p /usr/local \
+ARG Strelka2_VERSION=2.9.10
+RUN mamba create -qy -p /usr/local \
     -c bioconda \
     -c conda-forge \
-    tool_name==${TOOL_VERSION}
+    strelka==${Strelka2_VERSION}
 
 # Deploy the target tools into a base image
 FROM ubuntu:20.04
 COPY --from=builder /usr/local /usr/local
 
-LABEL maintainer="Your Name <YourName@mednet.ucla.edu>"
+LABEL maintainer="Mao Tian <maotian@mednet.ucla.edu>"

README.md

@@ -1,38 +1,30 @@
-# docker-tool_name
-Template Repository for the Boutros Lab Dockerfiles based on the bl-base image.
+# docker-Strelka2
+Strelka2 is a tool for fast and accurate calling of germline and somatic variants. To execute Strelka2, a matched normal sample, a `normal.bam`, and a reference fasta are needed to distinguish both germline variation and sequencing artifacts. The output of Strelka2 includes variant predictions, `.vcf.gz` files, and statistics, `.tsv` files. For more input requirements and output file formats, please visit [Strelka2 user guide](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md).
 
-The bl-base image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/bl-base
+The Strelka2 image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/strelka2
 
 # Documentation
-Docker introduction [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+Introduction)
-
-Dockerfile Best Practices [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Dockerfile+Best+Practices)
-
-Docker image versioning standard [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization)
-
+The main github page of Strelka2 can be found [here](https://github.com/Illumina/strelka). For execution and run options, please consult the Strelka2 user manual is [here](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md).
 
 # Version
 | Tool | Version |
 |------|---------|
-|tool_name| X.X.X|
-|tool_name_2|X.X.X|
-
+|Strelka2| 2.9.10|
 
 ---
 
 ## References
 
-1. Tool specific references can be listed here
-
+1. Kim, S., Scheffler, K., Halpern, A.L. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods 15, 591–594 (2018). https://doi.org/10.1038/s41592-018-0051-x
 ---
 
 ## License
 
-Author: Name1, Name2
+Author: Mao Tian, Caden Bugh.
 
-[docker repo name] is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
+docker-Strelka2 is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
 
-<one line to give the program's name and a brief idea of what it does.>
+docker-Strelka2 is a tool for fast and accurate calling of germline and somatic variants
 
 Copyright (C) 2021 University of California Los Angeles ("Boutros Lab") All rights reserved.
 

metadata.yaml

@@ -1,10 +1,10 @@
 ---
 Category: 'docker'
-Description: 'Template Docker repository for tool_name'  # Description of why the repository exists
-Maintainers: ['YourName@mednet.ucla.edu']  # email address of maintainers
-Contributors: ['Your Name']  # Full names of contributors
+Description: 'Docker repository for Strelka2'  # Description of why the repository exists
+Maintainers: ['maotian@mednet.ucla.edu']  # email address of maintainers
+Contributors: ['Mao Tian']  # Full names of contributors
 Languages: ['Dockerfile']  # programming languages used
-Tools: ['tool_name']  # Name of the tool(s) used in the Dockerfile
-Version: ['X.X.X']  # Tool version number
-Purpose of tool: ''  # Description of what this tool does
-References: ''  # is the tool/dependencies published, is there a confluence page
+Tools: ['Strelka2']  # Name of the tool(s) used in the Dockerfile
+Version: ['2.9.10']  # Tool version number
+Purpose of tool: 'Strelka calls somatic and germline small variants from mapped sequencing reads'  # Description of what this tool does
+References: 'Kim, S., Scheffler, K., Halpern, A.L. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods 15, 591–594 (2018). https://doi.org/10.1038/s41592-018-0051-x'  # is the tool/dependencies published, is there a confluence page