biowdl/sequence-classification

A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample

sequence-classification

This repository contains the Biowdl workflow usable for processing metagenomics data sets using centrifuge and krona.

Documentation

Documentation for this workflow can be found here.

About

This workflow is part of Biowdl developed by the SASC team at Leiden University Medical Center.

Contact

For any question related to sequence-classification, please use the github issue tracker or contact the SASC team directly at: [email protected].

sequence-classification's Issues

Release 1.0.0

First release checklist

• Make sure a gh-pages branch is setup.
  • Contains the index.html.
  • The values in the _config.yml are correct.
• Make sure Zenodo is enabled for the repo.
  • Switch on at https://zenodo.org/account/settings/github/.
  • Make sure the zenodo record ID is set in the _config.yml on the gh-pages branch. This ID can be found by clicking on the DOI badge displayed under the relevant repo at https://zenodo.org/account/settings/github/. The number in the urls that get displayed is the number that should be put into the config.
• Check that the repository tagline has the appropriate category at the end, eg. Category: Multi-Sample.
• Follow the general checklist.
• Update the biowdl homepage, by pushing on empty commit to the master branch of biowdl/biowdl.github.io.

General release checklist

• Check outstanding issues on JIRA and Github
• Update all submodules to latest master with: git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
• check all submodules are tagged correctly with git submodule
• run tests to confirm to be released version works.
• Generate inputs overview using wdl-aid:
  wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
• Publish documentation (updateDocs.sh) from develop branch
  • Copy docs folder to gh-pages branch
  • Overwrite existing develop folder with docs folder on gh-pages
  • Push changes to gh-pages branch
• Check latest documentation
  looks fine
• Change current development version in CHANGELOG.md to stable version.
• Run the release script release.sh
  • Check all submodules are tagged
  • Merge the develop branch into master
  • Created an annotated tag with the stable version number. Include changes
    from changelog.md.
  • Confirm or set stable version to be used for tagging
  • Push tag to remote.
  • Merge master branch back into develop.
  • Add updated version number to develop
• Publish documentation (updateDocs.sh) from master branch
  • Copy docs folder to gh-pages branch
  • Rename docs to new stable version on gh-pages
  • Set latest version to new version
  • Push changes to gh-pages branch
• Create a new release from the pushed tag on github
• Prepare the repo for packaging by git checkout master && git submodule update --init --recursive
  • Package the wdl files with wdl-packager --reproducible -a LICENSE -a dockerImages.yml <WDL_FILE>
  • Add the package(s) to the github release. Also add the original WDL file
    as <pipeline>_<version>.wdl following the same naming as the package.
    This alllows for usage of wdl and imports zip with cromwell without
    requiring the user to extract the package.