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‎cwltool/schemas/.gitignore

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*~
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*.pyc
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*.egg
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*.egg-info
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.idea/*
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common-workflow-language.github.io/
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cwltool/

‎cwltool/schemas/CITATION

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To cite the Common Workflow Language standard in a publication, please use:
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Amstutz, Peter; Andeer, Robin; Chapman, Brad; Chilton, John; Crusoe, Michael
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R.; Valls Guimerà, Roman; Carrasco Hernandez, Guillermo; Ivkovic, Sinisa;
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Kartashov, Andrey; Kern, John; Leehr, Dan; Ménager, Hervé; Mikheev, Maxim;
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Pierce, Tim; Randall, Josh; Soiland-Reyes, Stian; Stojanovic, Luka; Tijanić,
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Nebojša (2016): Common Workflow Language, draft 3. figshare.
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https://dx.doi.org/10.6084/m9.figshare.3115156.v1
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@data{common-workflow-language-draft3,
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doi = {10.6084/m9.figshare.3115156.v1},
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url = {http://dx.doi.org/10.6084/m9.figshare.3115156.v1},
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author = {Peter Amstutz; Robin Andeer; Brad Chapman; John Chilton;
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Michael R. Crusoe; Roman Valls Guimerà; Guillermo Carrasco Hernandez;
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Sinisa Ivkovic; Andrey Kartashov; John Kern; Dan Leehr; Hervé Ménager;
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Maxim Mikheev; Tim Pierce; Josh Randall; Stian Soiland-Reyes; Luka Stojanovic;
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Nebojša Tijanić; },
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publisher = {Figshare},
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title = {Common Workflow Language, draft 3},
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year = {2016}
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}

‎cwltool/schemas/CODE_OF_CONDUCT.md

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CWL Code of Conduct
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===================
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The CWL Project is dedicated to providing a harassment-free experience for
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everyone. We do not tolerate harassment of participants in any form.
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This code of conduct applies to all CWL Project spaces both online and off: the
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Google Group, the Gitter chat room, the Google Hangouts chats, and any other
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CWL spaces. Anyone who violates this code of conduct may be sanctioned or
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expelled from these spaces at the discretion of the CWL Leadership Team.
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Some CWL Project spaces may have additional rules in place, which will be
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made clearly available to participants. Participants are responsible for
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knowing and abiding by these rules.
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Harassment includes, but is not limited to:
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- Offensive comments related to gender, gender identity and expression, sexual
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orientation, disability, mental illness, neuro(a)typicality, physical
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appearance, body size, age, race, or religion.
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- Unwelcome comments regarding a person’s lifestyle choices and practices,
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including those related to food, health, parenting, drugs, and employment.
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- Deliberate misgendering or use of [dead](https://www.quora.com/What-is-deadnaming/answer/Nancy-C-Walker)
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or rejected names.
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- Gratuitous or off-topic sexual images or behaviour in spaces where they’re not
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appropriate.
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- Physical contact and simulated physical contact (eg, textual descriptions like
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“\*hug\*” or “\*backrub\*”) without consent or after a request to stop.
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- Threats of violence.
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- Incitement of violence towards any individual, including encouraging a person
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to commit suicide or to engage in self-harm.
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- Deliberate intimidation.
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- Stalking or following.
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- Harassing photography or recording, including logging online activity for
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harassment purposes.
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- Sustained disruption of discussion.
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- Unwelcome sexual attention.
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- Pattern of inappropriate social contact, such as requesting/assuming
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inappropriate levels of intimacy with others
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- Continued one-on-one communication after requests to cease.
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- Deliberate “outing” of any aspect of a person’s identity without their consent
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except as necessary to protect vulnerable people from intentional abuse.
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- Publication of non-harassing private communication.
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The CWL Project prioritizes marginalized people’s safety over privileged
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people’s comfort. The CWL Leadeship Team will not act on complaints regarding:
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- ‘Reverse’ -isms, including ‘reverse racism,’ ‘reverse sexism,’ and ‘cisphobia’
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- Reasonable communication of boundaries, such as “leave me alone,” “go away,” or
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“I’m not discussing this with you.”
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- Communicating in a [tone](http://geekfeminism.wikia.com/wiki/Tone_argument)
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you don’t find congenial
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Reporting
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---------
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If you are being harassed by a member of the CWL Project, notice that someone
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else is being harassed, or have any other concerns, please contact the CWL
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Leadership Team at [email protected]. If person who is harassing
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you is on the team, they will recuse themselves from handling your incident. We
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will respond as promptly as we can.
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This code of conduct applies to CWL Project spaces, but if you are being
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harassed by a member of CWL Project outside our spaces, we still want to
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know about it. We will take all good-faith reports of harassment by CWL Project
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members, especially the CWL Leadership Team, seriously. This includes harassment
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outside our spaces and harassment that took place at any point in time. The
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abuse team reserves the right to exclude people from the CWL Project based on
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their past behavior, including behavior outside CWL Project spaces and
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behavior towards people who are not in the CWL Project.
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In order to protect volunteers from abuse and burnout, we reserve the right to
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reject any report we believe to have been made in bad faith. Reports intended
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to silence legitimate criticism may be deleted without response.
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We will respect confidentiality requests for the purpose of protecting victims
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of abuse. At our discretion, we may publicly name a person about whom we’ve
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received harassment complaints, or privately warn third parties about them, if
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we believe that doing so will increase the safety of CWL Project members or
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the general public. We will not name harassment victims without their
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affirmative consent.
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Consequences
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------------
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Participants asked to stop any harassing behavior are expected to comply
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immediately.
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If a participant engages in harassing behavior, the CWL Leadership Team may
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take any action they deem appropriate, up to and including expulsion from all
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CWL Project spaces and identification of the participant as a harasser to other
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CWL Project members or the general public.
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This anti-harassment policy is based on the [example policy from the Geek
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Feminism wiki](http://geekfeminism.wikia.com/wiki/Community_anti-harassment/Policy),
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created by the Geek Feminism community.
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CWL Leadership Team
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-------------------
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As a stop gap measure until a more formal governance structure is adopted, the
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following individuals make up the leadership of the CWL Project: Peter Amstutz,
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John Chilton, Michael R. Crusoe, and Nebojša Tijanić.
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To report an issue with anyone on the team you can escalate to Ward Vandewege
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(Curoverse) [email protected], Anton Nekrutenko (Galaxy)
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anton AT bx DOT psu DOT edu, C. Titus Brown (UC Davis) [email protected], or
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Brandi Davis-Dusenbery (Seven Bridges Genomics) [email protected].

‎cwltool/schemas/CONFORMANCE_TESTS.md

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# Common workflow language conformance test suite
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The conformance tests are intended to test feature coverage of a CWL
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implementation. It uses the module "cwltool.cwltest" from the cwltool
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reference implementation.
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## Usage
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```
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$ ./run_test.sh
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--- Running conformance test draft-3 on cwl-runner ---
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Test [49/49]
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All tests passed
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```
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By default, `run_test.sh` will test `cwl-runner` in $PATH against the current
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stable CWL draft.
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## Options
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RUNNER=other-cwl-runner
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The CWL implementation to be tested.
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DRAFT=draft-N
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The CWL draft to be tested.
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-nN
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Run a single specific test number N.
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For example, to run conformance test 15 of draft-2 against the "cwltool"
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reference implementation:
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```
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$ ./run_test.sh RUNNER=cwltool DRAFT=draft-2 -n15
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Test [15/49]
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All tests passed
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```
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## Notes
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_NOTE_: For running on OSX systems, you'll need to install coreutils via brew. This will add to your
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system some needed GNU-like tools like `greadlink`.
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1. If you haven't already, install [brew](http://brew.sh/) package manager in your mac
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2. Run `brew install coreutils`

‎cwltool/schemas/LICENSE.txt

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