I am likely to write a few generic WDL tasks as part of my own work. Is this repo suitable for contributions, or are these tasks specific to your project?

https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#true-and-false

At lines 47-49 you're using integer values. The spec states that they must be String values.

We received this e-mail from a user:

First, just wanted to say I love the BioWDL project. Very helpful and the code is well organized. I am having trouble getting any BioWDL tasks to run on a cromwell instance on AWS. It seems to work fine if the runtime memory is changed to "3G" or some string with a "GB" or "MB" unit, but fails if the current setup with an integer value is used. Is there a setting I should be using on cromwell to default the units to GB? Mind sharing what that runtime value is? I can't seem to find anything in the cromwell docs. Thanks

We should change memory runtime attributes to strings so this works cross-platform.

On line 62, singleCell is used as a placeholder expression with true and false options. singleCell is type Boolean? but true/false options can only be used with type Boolean. Change to ~{true="--sc" false="" select_first([singleCell])}. If singleCell is undefined, the placeholder is replaced by the empty string. This is implied a couple of places in the 1.0 spec and made explicit in 1.1.

I was just battening down miniwdl's parsing of escape sequences in string literals, and got tripped up here:

Looking at the WDL spec on escape sequences, do you think there should be a double-backslash instead of single here? (Would that break it?)

• 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.

Around here there are unzip/zip flags used. These might be redundant:

Because you can cat gzip/bzip2 files and it treats it as a single file (not mixed types though):
https://stackoverflow.com/questions/8005114/fast-concatenation-of-multiple-gzip-files

Especially the unzip flag the zip flag might be used.

• 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.

key R1 is supplied twice:

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

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

Release checklist

• Check outstanding issues on JIRA and Github
• 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
• 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.
• 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

Release checklist

• Check outstanding issues on JIRA and Github
• 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