This pull request (PR) contains a Dockerfile that builds an ubuntu image for running the WGS Bovine-TB bioinformatics pipeline (~2.83Gb). It installs nextflow as well as the tools defined in Install_dependencies.sh
File Changes:
Created Dockerfile for building the pipeline
Moved the commands that download test data at the end of Install_dependancies.sh into download-test-data.sh. This was done to decrease docker build times and decrease image size.
Updated Readme.md with docker build instructions
Nextflow install script pulled from https://get.nextflow.io into install_nextflow-20.7.1.bash
As this is your first PR, a few review guidelines:
Mergability. The dev should do this but make sure there aren't merge conflicts (github will tell you)
Tests. The dev should also do this, but make sure the CI tests pass (github will tell you when CircleCI is up and running).
Size. Generally, PRs should be small (sometimes as small as a single line). Large PRs (> several hundred lines) are exponentially longer to read, understand and review. It's ok if the PR feature is just a small step toward a larger feature, so long as its contribution is specific, logical and the doesn't break the codebase! It's good practice to match PRs to Jira tasks. This PR is large because of install_nextflow-20.7.1.bash, my additions are only around 100 lines.
Read. Check that you understand what the code is doing on at least a high-level
Feedback. You can attach feedback on specific lines via github
Neatness. While the PR might be small, the code should be neat, well-commented and conform to style guidelines. This ensures that codebase cleanliness is maintained.
Bugs. Look for any possible bugs. If it's decided a bugfix should be left for a future PR, a comment starting with BUG: should be left in the code and recorded on github/jira.
Request changes. If the PR requires further changes following review, let the dev know (or select 'request changes' on github) so they can update their branch. The dev then requests the reviewer for rereview when they're ready.
Approval and merge. When you're happy with the PR, approve it on github and leave a comment (can be as small as "nice PR!"). Let the dev know so they can merge it into master and update Jira.
This pull request (PR) contains a
Dockerfilethat builds an ubuntu image for running the WGS Bovine-TB bioinformatics pipeline (~2.83Gb). It installs nextflow as well as the tools defined inInstall_dependencies.shFile Changes:
Dockerfilefor building the pipelineInstall_dependancies.shintodownload-test-data.sh. This was done to decrease docker build times and decrease image size.Readme.mdwith docker build instructionshttps://get.nextflow.iointoinstall_nextflow-20.7.1.bashAs this is your first PR, a few review guidelines:
install_nextflow-20.7.1.bash, my additions are only around 100 lines.BUG:should be left in the code and recorded on github/jira.For more information see: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-request-reviews