reference correct branch, remove carpentries refs (#223)

* Update CITATION with CACM paper

Author: mr-c

.travis.yml

@@ -10,7 +10,7 @@ cache:
 
 branches:
   only:
-    - gh-pages
+    - main
     - /.*/
 
 before_script:

16-file-formats/index.md

@@ -54,11 +54,11 @@ parameterization.
 :language: yaml
 ```
 
-___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from [https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/16-file-formats/file-formats.bam
-](https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/16-file-formats/file-formats.bam) and can be downloaded e.g. via `wget`:
+___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from [https://github.com/common-workflow-language/user_guide/raw/main/_includes/cwl/16-file-formats/file-formats.bam
+](https://github.com/common-workflow-language/user_guide/raw/main/_includes/cwl/16-file-formats/file-formats.bam) and can be downloaded e.g. via `wget`:
 
 ```bash
-wget https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/16-file-formats/file-formats.bam
+wget https://github.com/common-workflow-language/user_guide/raw/main/_includes/cwl/16-file-formats/file-formats.bam
 ```
 
 Now invoke `cwl-runner` with the tool wrapper and the input object on the

19-custom-types/index.md

@@ -36,10 +36,10 @@ converting a standard biom table file to hd5 format.
 :language: yaml
 ```
 
-___Note:___ To follow the example below, you need to download the example input file, *rich_sparse_otu_table.biom*. The file is available from [https://raw.githubusercontent.com/common-workflow-language/user_guide/gh-pages/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom](https://raw.githubusercontent.com/common-workflow-language/user_guide/gh-pages/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom) and can be downloaded e.g. via `wget`:
+___Note:___ To follow the example below, you need to download the example input file, *rich_sparse_otu_table.biom*. The file is available from [https://raw.githubusercontent.com/common-workflow-language/user_guide/main/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom](https://raw.githubusercontent.com/common-workflow-language/user_guide/main/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom) and can be downloaded e.g. via `wget`:
 
 ```bash
-wget https://raw.githubusercontent.com/common-workflow-language/user_guide/gh-pages/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom
+wget https://raw.githubusercontent.com/common-workflow-language/user_guide/main/_includes/cwl/19-custom-types/rich_sparse_otu_table.biom
 ```
 
 On line 29, in `inputs:table_type`, a list of allowable table options to be used in the

21-1st-workflow/index.md

@@ -25,7 +25,7 @@ compiles it.
 ```
 
 ```{admonition} Visualization of 1st-workflow.cwl
-[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/21-1st-workflow/1st-workflow.cwl)
+[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/main/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/main/_includes/cwl/21-1st-workflow/1st-workflow.cwl)
 ```
 
 Use a YAML or a JSON object in a separate file to describe the input of a run:

22-nested-workflows/index.md

@@ -45,11 +45,11 @@ the `compile` step in orange; `compile` is another workflow, diagrammed on the
 right. In purple we see the fixed string `"Hello.java"` being supplied as the
 `name_of_file_to_extract`.
 
-<a href="https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/22-nested-workflows/nestedworkflows.cwl"><img
-src="https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/22-nested-workflows/nestedworkflows.cwl"
+<a href="https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/main/_includes/cwl/22-nested-workflows/nestedworkflows.cwl"><img
+src="https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/main/_includes/cwl/22-nested-workflows/nestedworkflows.cwl"
 alt="Visualization of nestedworkflows.cwl" /></a>
-<a href="https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/22-nested-workflows/1st-workflow.cwl"><img
-src="https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/22-nested-workflows/1st-workflow.cwl"
+<a href="https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/main/_includes/cwl/22-nested-workflows/1st-workflow.cwl"><img
+src="https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/main/_includes/cwl/22-nested-workflows/1st-workflow.cwl"
 alt="Visualization of 1st-workflow.cwl" /></a>
 ```
 

CITATION

@@ -1,6 +1,29 @@
 # Citation
 
-To cite CWL as a project, as a language, or as a standard, use:
+To cite the Common Workflow Language  and the CWL project in a scholary work, please use:
+
+Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, and The CWL Community. 2022. Methods included: standardizing computational reuse and portability with the Common Workflow Language. Commun. ACM 65, 6 (June 2022), 54–63. https://doi.org/10.1145/3486897
+
+@article{10.1145/3486897,
+author = {Crusoe, Michael R. and Abeln, Sanne and Iosup, Alexandru and Amstutz, Peter and Chilton, John and Tijani\'{c}, Neboj\v{s}a and M\'{e}nager, Herv\'{e} and Soiland-Reyes, Stian and Gavrilovi\'{c}, Bogdan and Goble, Carole and Community, The CWL},
+title = {Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language},
+year = {2022},
+issue_date = {June 2022},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+volume = {65},
+number = {6},
+issn = {0001-0782},
+url = {https://doi.org/10.1145/3486897},
+doi = {10.1145/3486897},
+abstract = {Standardizing computational reuse and portability with the Common Workflow Language.},
+journal = {Commun. ACM},
+month = {may},
+pages = {54–63},
+numpages = {10}
+}
+
+To cite just the CWL standards themselves, please use the following inclusive of the DOI:
 
 Amstutz, Peter; Crusoe, Michael R; Tijanić, Nebojša; Chapman, Brad;
 Chilton, John; Heuer, Michael; Kartashov, Andrey; Kern, John; Leehr, Dan;
@@ -23,12 +46,9 @@ Luka Stojanovic
   year = {2016}
 }
 
-# the above is from https://github.com/common-workflow-language/common-workflow-language/blob/master/CITATION
+# the above is from https://github.com/common-workflow-language/common-workflow-language/blob/main/CITATION
 
 Our preferred DOI for the "CWL User Guide" is http://doi.org/10.5281/zenodo.840129
 
 The latest DOI for the "CWL User Guide" is:
 [![DOI](https://zenodo.org/badge/89621457.svg)](https://zenodo.org/badge/latestdoi/89621457)
-
-The structure and style of this user guide is derived from [the Carpentries](https://github.com/carpentries)
-lesson template: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.838778.svg)](https://doi.org/10.5281/zenodo.838778)

CONTRIBUTING.md

@@ -2,7 +2,7 @@
 
 The [Common Workflow Language project][cwl-site] is an open source project,
 and we welcome contributions of all kinds:
-new lessons,
+new sections,
 fixes to existing material,
 bug reports,
 and reviews of proposed changes are all welcome.
@@ -43,32 +43,10 @@ and to meet some of our community members.
     you can submit a pull request (PR).
     Instructions for doing this are [included below][#using-github].
 
-## Where to Contribute
-
-1.  If you wish to change this lesson,
-    please work in <https://github.com/common-workflow-language/user_guide>,
-    which can be viewed at <https://www.commmonwl.org/user_guide/>.
-
-2.  If you wish to change the example lesson,
-    please work in <https://github.com/carpentries/lesson-example>,
-    which documents the format of our lessons
-    and can be viewed at <https://carpentries.github.io/lesson-example>.
-
-3.  If you wish to change the template used for workshop websites,
-    please work in <https://github.com/carpentries/workshop-template>.
-    The home page of that repository explains how to set up workshop websites,
-    while the extra pages in <https://carpentries.github.io/workshop-template>
-    provide more background on our design choices.
-
-4.  If you wish to change CSS style files, tools,
-    or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
-    please work in <https://github.com/carpentries/styles>.
-
 ## What to Contribute
 
 There are many ways to contribute,
-from writing new exercises and improving existing ones
-to updating or filling in the documentation
+like updating or filling in the documentation
 and submitting [bug reports][issues]
 about things that don't work, aren't clear, or are missing.
 If you are looking for ideas,
@@ -78,52 +56,33 @@ or the issues for [Common Workflow Language][cwl-issues] project itself.
 Comments on issues and reviews of pull requests are just as welcome:
 we are smarter together than we are on our own.
 Reviews from novices and newcomers are particularly valuable:
-it's easy for people who have been using these lessons for a while
+it's easy for people who have been using these materials for a while
 to forget how impenetrable some of this material can be,
 so fresh eyes are always welcome.
 
-<!--
-## What *Not* to Contribute
-
-Our lessons already contain more material than we can cover in a typical workshop,
-so we are usually *not* looking for more concepts or tools to add to them.
-As a rule,
-if you want to introduce a new idea,
-you must (a) estimate how long it will take to teach
-and (b) explain what you would take out to make room for it.
-The first encourages contributors to be honest about requirements;
-the second, to think hard about priorities.
-
-We are also not looking for exercises or other material that only run on one platform.
-Our workshops typically contain a mixture of Windows, macOS, and Linux users;
-in order to be usable,
-our lessons must run equally well on all three.
--->
 ## Using GitHub
 
 If you choose to contribute via GitHub, you may want to look at
 [How to Contribute to an Open Source Project on GitHub][how-contribute].
 To manage changes, we follow [GitHub flow][github-flow].
-Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
-The maintainers are community volunteers and have final say over what gets merged into the lesson.
-To use the web interface for contributing to a lesson:
+To use the web interface for contributing:
 
 1.  Fork the originating repository to your GitHub profile.
-2.  Within your version of the forked repository, move to the `gh-pages` branch and
+2.  Within your version of the forked repository, move to the `main` branch and
 create a new branch for each significant change being made.
 3.  Navigate to the file(s) you wish to change within the new branches and make revisions as required.
 4.  Commit all changed files within the appropriate branches.
 5.  Create individual pull requests from each of your changed branches
-to the `gh-pages` branch within the originating repository.
+to the `main` branch within the originating repository.
 6.  If you receive feedback, make changes using your issue-specific branches of the forked
 repository and the pull requests will update automatically.
 7.  Repeat as needed until all feedback has been addressed.
 
-When starting work, please make sure your clone of the originating `gh-pages` branch is up-to-date
+When starting work, please make sure your clone of the originating `main` branch is up-to-date
 before creating your own revision-specific branch(es) from there.
 Additionally, please only work from your newly-created branch(es) and *not*
-your clone of the originating `gh-pages` branch.
-Lastly, published copies of all the lessons are available in the `gh-pages` branch of the originating
+your clone of the originating `main` branch.
+Lastly, published copies of all the sections are available in the `main` branch of the originating
 repository for reference while revising.
 
 ## Other Resources
@@ -132,17 +91,11 @@ General discussion of [Common Workflow Language][cwl-site] project
 happens on the [discussion mailing list][discuss-list],
 which everyone is welcome to join.
 
-[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
-[dc-lessons]: http://datacarpentry.org/lessons/
-[dc-site]: http://datacarpentry.org/
 [discuss-list]: https://groups.google.com/forum/#!forum/common-workflow-language
 [github]: https://github.com
 [github-flow]: https://guides.github.com/introduction/flow/
 [github-join]: https://github.com/join
 [how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
 [issues]: https://github.com/common-workflow-language/user_guide/issues
 [repo]: https://github.com/common-workflow-language/user_guide
-[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: https://software-carpentry.org/lessons/
-[swc-site]: https://software-carpentry.org/
 [cwl-site]: https://www.commonwl.org/

LICENSE.md

@@ -2,10 +2,6 @@
 
 ## Instructional Material
 
-This material is derived from a framework created by the Software Carpentry
-and Data Carpentry projects under the [Creative Commons Attribution
-license][cc-by-human].
-
 All Common Workflow Language project instructional material and changes
 to the structure are also made available under the [Creative Commons Attribution
 license][cc-by-human]. The following is a human-readable summary of
@@ -26,8 +22,8 @@ Under the following terms:
 
 * **Attribution**---You must give appropriate credit (mentioning that
   your work is derived from work that is Copyright © the Common Workflow
-  Language project, and Copyright © Software Carpentry, and, where practical, linking to
-  https://www.commonwl.org/ and https://software-carpentry.org/), provide a [link to the
+  Language project, and, where practical, linking to
+  https://www.commonwl.org/ ), provide a [link to the
   license][cc-by-human], and indicate if changes were made. You may do
   so in any reasonable manner, but not in any way that suggests the
   licensor endorses you or your use.
@@ -61,12 +57,9 @@ limitations under the License.
 
 ## Trademark
 
-"Software Carpentry" and "Data Carpentry" and their respective logos
-are registered trademarks of [Community Initiatives][CI].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
 [apache-2.0-license]: https://opensource.org/licenses/Apache-2.0
 [mit-license]: https://opensource.org/licenses/mit-license.html
-[ci]: http://communityin.org/
 [osi]: https://opensource.org

README.md

@@ -1,6 +1,6 @@
 [![DOI](https://zenodo.org/badge/89621457.svg)](https://zenodo.org/badge/latestdoi/89621457)
 
-[![Syntax Check](https://travis-ci.org/common-workflow-language/user_guide.svg?branch=gh-pages)](https://travis-ci.org/common-workflow-language/user_guide)
+[![Syntax Check](https://travis-ci.org/common-workflow-language/user_guide.svg?branch=main)](https://travis-ci.org/common-workflow-language/user_guide)
 
 [User guide for CWL v1.0.2](https://www.commonwl.org/user_guide/)
 
@@ -9,30 +9,20 @@ https://github.com/common-workflow-language/common-workflow-language/blob/a2a8a0
 
 ## Contributing
 
-We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any
+We welcome all contributions to improve the materials! Maintainers will do their best to help you if you have any
 questions, concerns, or experience any difficulties along the way.
 To edit the user guide:
 
-We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at
-the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
-how to write new episodes.
+We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md).
 
-- The text files for each tutorial can be found in the directory [_episodes](/_episodes/index.md)
-
-- The cwl and yaml code files linked to each tutorial can be found in the directory [_includes/cwl](https://github.com/common-workflow-language/user_guide/tree/gh-pages/_includes/cwl)
-
-This repo is based upon https://github.com/swcarpentry/styles and should be periodically resynced.
-
-## Maintainer(s)
 
 * FIXME
 
 ## Authors
 
-A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
+A list of contributors to these materials can be found in [AUTHORS](AUTHORS)
 
 ## Citation
 
-To cite this lesson, please consult with [CITATION](CITATION)
+To cite these materials, please consult with [CITATION](CITATION)
 
-[lesson-example]: https://carpentries.github.io/lesson-example