merged recent changes from gh-pages

Toby Hodges · Toby Hodges · commit 4c999cdf4c3d · 2017-08-08T15:37:12.000+02:00
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -1,9 +0,0 @@
-Please delete the text below before submitting your contribution. 
-
----
-
-Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
-
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  
-
----
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,9 +0,0 @@
-Please delete the text below before submitting your contribution. 
-
----
-
-Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
-
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  
-
----
diff --git a/_episodes/16-file-formats.md b/_episodes/16-file-formats.md
@@ -19,7 +19,8 @@ type-checking when creating parameter files.
 For file formats, we recommend referencing existing ontologies (like EDAM in
 our example), reference a local ontology for your institution, or do not add
 a file format initially for quick development before sharing your tool with
-others.
+others. You can browse existing file format listings for IANA [here][IANA] and
+for EDAM [here][EDAM].
 
 Note that for added value `cwltool` can do some basic reasoning based on file
 formats and warn you if there seem to be some obvious mismatches.
@@ -49,12 +50,12 @@ Now invoke `cwl-runner` with the tool wrapper and the input object on the
 command line:
 
 ~~~
-$ cwltool metadata_example.cwl sample.json
+$ cwltool metadata_example.cwl sample.yml
 /usr/local/bin/cwltool 1.0.20161114152756
 Resolved 'metadata_example.cwl' to 'file:///media/large_volume/testing/cwl_tutorial2/metadata_example.cwl'
 [job metadata_example.cwl] /tmp/tmpNWyAd6$ /bin/sh \
     -c \
-    'wc' '-l' '/tmp/tmpBf6m9u/stge293ac74-3d42-45c9-b506-dd35ea3e6eea/rna.SRR948778.bam' > /tmp/tmpNWyAd6/output.txt
+    'wc' '-l' '/tmp/tmpBf6m9u/stge293ac74-3d42-45c9-b506-dd35ea3e6eea/file-formats.bam' > /tmp/tmpNWyAd6/output.txt
 Final process status is success
 {
   "report": {
@@ -69,3 +70,6 @@ Final process status is success
 }
 ~~~
 {: .output}
+
+[IANA]: https://www.iana.org/assignments/media-types/media-types.xhtml
+[EDAM]: http://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_1915
diff --git a/_episodes/17-metadata.md b/_episodes/17-metadata.md
@@ -25,10 +25,9 @@ and workflows. This example includes metadata allowing others to cite your tool.
 
 *metadata_example2.cwl*
 
-~~~
+```
 {% include cwl/metadata_example2.cwl %}
-~~~
-{: .source}
+```
 
 #### Extended Example
 
@@ -39,9 +38,8 @@ requirements in order to use the tool, and a few more metadata fields.
 
 *metadata_example3.cwl*
 
-~~~
+```
 {% include cwl/metadata_example3.cwl %}
-~~~
-{: .source}
+```
 
 [schema-salad]: http://www.commonwl.org/v1.0/SchemaSalad.html#Explicit_context
diff --git a/_episodes/18-1st-workflow.md b/_episodes/18-1st-workflow.md
diff --git a/_episodes/19-nested-workflows.md b/_episodes/19-nested-workflows.md
diff --git a/_includes/cwl/1st-tool.cwl b/_includes/cwl/1st-tool.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/1st-workflow.cwl b/_includes/cwl/1st-workflow.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/_includes/cwl/arguments.cwl b/_includes/cwl/arguments.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 label: Example trivial wrapper for Java 7 compiler
diff --git a/_includes/cwl/array-inputs.cwl b/_includes/cwl/array-inputs.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/_includes/cwl/array-outputs.cwl b/_includes/cwl/array-outputs.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: touch
diff --git a/_includes/cwl/createfile.cwl b/_includes/cwl/createfile.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 class: CommandLineTool
 cwlVersion: v1.0
 baseCommand: ["cat", "example.conf"]
diff --git a/_includes/cwl/docker.cwl b/_includes/cwl/docker.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: node
diff --git a/_includes/cwl/env.cwl b/_includes/cwl/env.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: env
diff --git a/_includes/cwl/expression.cwl b/_includes/cwl/expression.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/file-formats.bam b/_includes/cwl/file-formats.bam
diff --git a/_includes/cwl/inp.cwl b/_includes/cwl/inp.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/linkfile.cwl b/_includes/cwl/linkfile.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 hints:
diff --git a/_includes/cwl/metadata_example.cwl b/_includes/cwl/metadata_example.cwl
@@ -0,0 +1,28 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: An example tool demonstrating metadata.
+
+inputs:
+  aligned_sequences:
+    type: File
+    label: Aligned sequences in BAM format
+    format: edam:format_2572
+    inputBinding:
+      position: 1
+
+baseCommand: [ wc, -l ]
+
+stdout: output.txt
+
+outputs:
+  report:
+    type: stdout
+    format: edam:format_1964
+    label: A text file that contains a line count
+
+$namespaces:
+  edam: http://edamontology.org/
+$schemas:
+  - http://edamontology.org/EDAM_1.18.owl
diff --git a/_includes/cwl/metadata_example2.cwl b/_includes/cwl/metadata_example2.cwl
@@ -0,0 +1,49 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: An example tool demonstrating metadata.
+doc: Note that this is an example and the metadata is not necessarily consistent.
+
+inputs:
+  aligned_sequences:
+    type: File
+    label: Aligned sequences in BAM format
+    format: edam:format_2572
+    inputBinding:
+      position: 1
+
+baseCommand: [ wc, -l ]
+
+stdout: output.txt
+
+outputs:
+  report:
+    type: stdout
+    format: edam:format_1964
+    label: A text file that contains a line count
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-6130-1021
+    s:email: mailto:dyuen@oicr.on.ca
+    s:name: Denis Yuen
+
+s:contributor:
+  - class: s:Person
+    s:identifier: http://orcid.org/0000-0002-7681-6415
+    s:email: mailto:briandoconnor@gmail.com
+    s:name: Brian O'Connor
+
+s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
+s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
+s:dateCreated: "2016-12-13"
+s:license: https://www.apache.org/licenses/LICENSE-2.0
+
+$namespaces:
+  s: https://schema.org/
+  edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/docs/schema_org_rdfa.html
+ - http://edamontology.org/EDAM_1.18.owl
diff --git a/_includes/cwl/metadata_example3.cwl b/_includes/cwl/metadata_example3.cwl
@@ -0,0 +1,56 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: An example tool demonstrating metadata.
+doc: Note that this is an example and the metadata is not necessarily consistent.
+
+hints:
+  ResourceRequirement:
+    coresMin: 4
+
+inputs:
+  aligned_sequences:
+    type: File
+    label: Aligned sequences in BAM format
+    format: edam:format_2572
+    inputBinding:
+      position: 1
+
+baseCommand: [ wc, -l ]
+
+stdout: output.txt
+
+outputs:
+  report:
+    type: stdout
+    format: edam:format_1964
+    label: A text file that contains a line count
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-6130-1021
+    s:email: mailto:dyuen@oicr.on.ca
+    s:name: Denis Yuen
+
+s:contributor:
+  - class: s:Person
+    s:identifier: http://orcid.org/0000-0002-7681-6415
+    s:email: mailto:briandoconnor@gmail.com
+    s:name: Brian O'Connor
+
+s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
+s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
+s:dateCreated: "2016-12-13"
+s:license: https://www.apache.org/licenses/LICENSE-2.0
+
+s:keywords: edam:topic_0091 , edam:topic_0622
+s:programmingLanguage: C
+
+$namespaces:
+ s: https://schema.org/
+ edam: https://edamontology.org/
+
+$schemas:
+ - https://schema.org/docs/schema_org_rdfa.html
+ - http://edamontology.org/EDAM_1.18.owl
diff --git a/_includes/cwl/nestedworkflows.cwl b/_includes/cwl/nestedworkflows.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: Workflow
 
diff --git a/_includes/cwl/record.cwl b/_includes/cwl/record.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/_includes/cwl/sample.yml b/_includes/cwl/sample.yml
@@ -0,0 +1,7 @@
+bam_input:
+    class: File
+    format: http://edamontology.org/format_2572
+    path: file-formats.bam
+bamstats_report:
+    class: File
+    path: /tmp/bamstats_report.zip
diff --git a/_includes/cwl/stdout.cwl b/_includes/cwl/stdout.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/_includes/cwl/tar-param.cwl b/_includes/cwl/tar-param.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: [tar, xf]
diff --git a/_includes/cwl/tar.cwl b/_includes/cwl/tar.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: [tar, xf]
diff --git a/setup.md b/setup.md
@@ -3,4 +3,20 @@ layout: page
 title: Setup
 permalink: /setup/
 ---
-FIXME
+To follow the Common Workflow Language user guide, you will need an up-to-date
+Linux or Mac OS X system, with the following software installed:
+
+- A text editor with YAML support
+- A CWL implementation to run the described tools and workflows. When first
+getting started with CWL, we recommend the reference implementation,
+[`cwltool`][ref-imp]. You can find a full list on
+[the project homepage][commonwl].
+- Most of the software tools used in the user guide are standard UNIX commands
+(`cat`, `echo`, `env`, `tar`, `touch`, `wc`), but to run all examples you will
+also need:
+  - node.js
+  - Java compiler
+  - Docker (optional)
+
+[ref-imp]: https://github.com/common-workflow-language/cwltool
+[commonwl]: http://www.commonwl.org/

-Original file line number
+Diff line change
@@ @@ -1,9 +0,0 @@ @@
 -Please delete the text below before submitting your contribution.
+-
 ----
+-
 -Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.
+-
 -Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).
+-
 ----
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+#!/usr/bin/env cwl-runner`
	`2`	`+`
`1`	`3`	`cwlVersion: v1.0`
`2`	`4`	`class: CommandLineTool`
`3`	`5`	`baseCommand: echo`