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View Code? Open in Web Editor NEWA collection of reusable WDL tasks. Category:Other
Home Page: https://biowdl.github.io/tasks/
License: MIT License
A collection of reusable WDL tasks. Category:Other
Home Page: https://biowdl.github.io/tasks/
License: MIT License
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.
key R1
is supplied twice:
Lines 180 to 183 in 46385dd
Around here there are unzip/zip flags used. These might be redundant:
Line 71 in c92755e
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.
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?
Release checklist
git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
git submodule
wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
updateDocs.sh
) from develop
branch
gh-pages
branchgh-pages
gh-pages branch
CHANGELOG.md
to stable version.release.sh
master
master
branch back into develop
.updateDocs.sh
) from master
branch
gh-pages
branchgh-pages
gh-pages branch
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.
Release checklist
updateDocs.sh
) from develop
branch
gh-pages
branchgh-pages
gh-pages branch
CHANGELOG.md
to stable version.release.sh
master
master
branch back into develop
.updateDocs.sh
) from master
branch
gh-pages
branchgh-pages
gh-pages branch
I was just battening down miniwdl's parsing of escape sequences in string literals, and got tripped up here:
Line 219 in c92755e
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?)
Release checklist
git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
git submodule
wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
updateDocs.sh
) from develop
branch
gh-pages
branchgh-pages
gh-pages branch
CHANGELOG.md
to stable version.release.sh
master
master
branch back into develop
.updateDocs.sh
) from master
branch
gh-pages
branchgh-pages
gh-pages branch
git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
git submodule
wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
updateDocs.sh
) from develop
branch
gh-pages
branchgh-pages
gh-pages branch
CHANGELOG.md
to stable version.release.sh
master
master
branch back into develop
.updateDocs.sh
) from master
branch
gh-pages
branchgh-pages
gh-pages branch
git checkout master && git submodule update --init --recursive
wdl-packager --reproducible -a LICENSE -a dockerImages.yml <WDL_FILE>
<pipeline>_<version>.wdl
following the same naming as the package.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.
git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
.git submodule
.wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
updateDocs.sh
) from develop
branch.
gh-pages
branch.gh-pages
.gh-pages branch
.CHANGELOG.md
to stable version.release.sh
.
master
.master
branch back into develop
.updateDocs.sh
) from master
branch.
gh-pages
branch.gh-pages
.gh-pages branch
.git checkout master && git submodule update --init --recursive
.
wdl-packager --reproducible -a LICENSE -a dockerImages.yml <WDL_FILE>
.<pipeline>_<version>.wdl
following the same naming as theRelease checklist
wdl-aid --strict -t scripts/docs_template.md.j2 pipeline.wdl > docs/inputs.md
updateDocs.sh
) from develop
branch
gh-pages
branchgh-pages
gh-pages branch
git submodule foreach "git checkout master;git pull; git submodule foreach --recursive 'git fetch'; git submodule update --init --recursive"
git submodule
CHANGELOG.md
to stable version.release.sh
master
master
branch back into develop
.updateDocs.sh
) from master
branch
gh-pages
branchgh-pages
gh-pages branch
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