Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of user_guide

user_guide - v0.4.1

Only small changes from 0.4.1, hoping to properly trigger Zenodo this time

What's Changed

  • Add clarity for installing dependencies and pip command for Graphviz by @AfiMaameDufie in https://github.com/common-workflow-language/user_guide/pull/304
  • Update code markdown using-containers.md by @khaiyra in https://github.com/common-workflow-language/user_guide/pull/306

New Contributors

  • @AfiMaameDufie made their first contribution in https://github.com/common-workflow-language/user_guide/pull/304
  • @khaiyra made their first contribution in https://github.com/common-workflow-language/user_guide/pull/306

Full Changelog: https://github.com/common-workflow-language/user_guide/compare/v0.4...v0.4.1

- Common Workflow Language
Published by mr-c over 3 years ago

user_guide - v0.4

What's Changed

  • Consistent formatting and additional array detail by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/26
  • Custom Types Lesson by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/27
  • Software Requirements Lesson by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/28
  • Fix input file parameter name by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/30
  • Fix record.cwl to make section 11 workable for record-job2.yml by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/35
  • added subworkflowfeaturerequirement note by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/40
  • Download link for file-formats.bam by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/41
  • Fix extension to yml by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/45
  • Fix typo by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/46
  • Add how to download test_proteins.fasta by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/47
  • Categorize the examples for each section by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/43
  • SPDX license identifiers by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/42
  • URL for the user guide changed by @BenjaminHCCarr in https://github.com/common-workflow-language/user_guide/pull/50
  • Add files for the examles in user guide by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/51
  • Add conformance test for section 4 using cwltest by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/52
  • Add .travis.yml to test the examples by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/53
  • move icons to a better place by @mr-c in https://github.com/common-workflow-language/user_guide/pull/56
  • Travis Badge on README by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/57
  • Fix branch parameter for travis badge by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/58
  • Enable CI for gh-pages by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/59
  • clarify CWL citation versus user guide citation by @mr-c in https://github.com/common-workflow-language/user_guide/pull/60
  • Fix #66 missing link for recommended practices by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/67
  • expand & correct list of expression capable fields by @mr-c in https://github.com/common-workflow-language/user_guide/pull/68
  • Update docker image for Java by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/69
  • suggestion for correction in introduction text by @hmenager in https://github.com/common-workflow-language/user_guide/pull/65
  • Add tests for the examples by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/61
  • Fix link and update tags to fit to example by @khillion in https://github.com/common-workflow-language/user_guide/pull/70
  • Update README.md by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/74
  • Update 07-containers.md by @jessMaia in https://github.com/common-workflow-language/user_guide/pull/78
  • Update 02-1st-example.md by @rmccole in https://github.com/common-workflow-language/user_guide/pull/79
  • Update 19-custom-types.md by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/83
  • Update custom-types.cwl by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/84
  • Update custom-types.yml by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/85
  • Update 02-1st-example.md by @rmccole in https://github.com/common-workflow-language/user_guide/pull/82
  • Update 03-input.md by @rmccole in https://github.com/common-workflow-language/user_guide/pull/81
  • Create biom-convert-table.yaml by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/87
  • Create richsparseotutable.biom by @sharmatime in https://github.com/common-workflow-language/userguide/pull/86
  • Update 16-file-formats.md by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/75
  • Fix indentation in 02-1st-example.md by @jirikuncar in https://github.com/common-workflow-language/user_guide/pull/88
  • Use released versions of cwltool, cwltest by @mr-c in https://github.com/common-workflow-language/user_guide/pull/93
  • Fix an example of Section7 not to use side effect by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/92
  • fix edam mismatch by @mr-c in https://github.com/common-workflow-language/user_guide/pull/97
  • Replace output identifier output with example_out by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/96
  • Fix the example for section 09 not to use side effect by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/94
  • Replace output identifier for section 7 with example_out by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/95
  • Add test for an example in Section 19 by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/102
  • Change the examples in Section 11 not to use side-effects by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/98
  • Change an example in Section 12 not to use side-effect by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/99
  • Change an example in section 13 not to use side-effect by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/100
  • Change an example in Section 14 not to use side-effect by @tom-tan in https://github.com/common-workflow-language/user_guide/pull/101
  • clean up syntax by @mr-c in https://github.com/common-workflow-language/user_guide/pull/105
  • Update 19-custom-types.md by @zipho in https://github.com/common-workflow-language/user_guide/pull/106
  • User permalink for original CWL user guide by @mr-c in https://github.com/common-workflow-language/user_guide/pull/109
  • List where parameter references & expressions are allowed by @mr-c in https://github.com/common-workflow-language/user_guide/pull/110
  • Update 09-array-inputs.md by @majensen in https://github.com/common-workflow-language/user_guide/pull/111
  • Fix bad heading in chapter 13 by @sersorrel in https://github.com/common-workflow-language/user_guide/pull/112
  • [ImgBot] optimizes images by @imgbot in https://github.com/common-workflow-language/user_guide/pull/113
  • add containers best practices by @mr-c in https://github.com/common-workflow-language/user_guide/pull/118
  • 16-file-formats: fix output name record by @jirikuncar in https://github.com/common-workflow-language/user_guide/pull/71
  • [WIP] Scatter guide by @biokcb in https://github.com/common-workflow-language/user_guide/pull/114
  • Update 16-file-formats.md by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/76
  • Fix wrong extension cwl -> yml in https://github.com/common-workflow-language/user_guide/pull/122
  • fix missing spdx link by @mr-c in https://github.com/common-workflow-language/user_guide/pull/123
  • Add visualization from view.commonwl.org by @mr-c in https://github.com/common-workflow-language/user_guide/pull/108
  • [ImgBot] Optimize images by @imgbot in https://github.com/common-workflow-language/user_guide/pull/124
  • Update 17-metadata.md by @sharmatime in https://github.com/common-workflow-language/user_guide/pull/77
  • Update 02-1st-example.md by @rmccole in https://github.com/common-workflow-language/user_guide/pull/80
  • Add filename by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/128
  • Add workflow filename by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/127
  • Fix typo by @alimanfoo in https://github.com/common-workflow-language/user_guide/pull/131
  • Expand create file example to show how to inject expressions into bash scripts in https://github.com/common-workflow-language/user_guide/pull/137
  • Update 02-1st-example.md by @longr in https://github.com/common-workflow-language/user_guide/pull/138
  • Update 04-output.md by @longr in https://github.com/common-workflow-language/user_guide/pull/139
  • Update episodes/21-1st-workflow.md by @emannuelOC in https://github.com/common-workflow-language/userguide/pull/145
  • Update 06-params.md by @longr in https://github.com/common-workflow-language/user_guide/pull/142
  • Update introductory text on landing page by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/149
  • YAML guide by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/151
  • Improve question wording by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/152
  • Typo by @kinow in https://github.com/common-workflow-language/user_guide/pull/153
  • encourage contributions from readers by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/154
  • WIP: Miscellaneous page by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/156
  • edit exampleoutput values by @tsuchi8 in https://github.com/common-workflow-language/userguide/pull/147
  • Update 14-runtime.md by @longr in https://github.com/common-workflow-language/user_guide/pull/144
  • Add Translation Button by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/133
  • Update 07-containers.md by @longr in https://github.com/common-workflow-language/user_guide/pull/143
  • About using hyphen as id by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/165
  • WORKAROUND for filename has space character by @manabuishii in https://github.com/common-workflow-language/user_guide/pull/164
  • explictly link to the extra docs by @mr-c in https://github.com/common-workflow-language/user_guide/pull/168
  • fix spelling by @wgerlach in https://github.com/common-workflow-language/user_guide/pull/169
  • Update from upstream by @mr-c in https://github.com/common-workflow-language/user_guide/pull/171
  • fix: Typo in container name by @ktaletsk in https://github.com/common-workflow-language/user_guide/pull/174
  • fix: Missing text typo by @ktaletsk in https://github.com/common-workflow-language/user_guide/pull/175
  • Typo: incorrect output parameter reference by @ktaletsk in https://github.com/common-workflow-language/user_guide/pull/178
  • Correct chapter reference and add link by @ktaletsk in https://github.com/common-workflow-language/user_guide/pull/179
  • Crosslinks for "Mapped Objects" section -> "Maps" by @stain in https://github.com/common-workflow-language/user_guide/pull/183
  • Correct link for yaml by @stain in https://github.com/common-workflow-language/user_guide/pull/182
  • typo in miscellaneous.md by @jjkoehorst in https://github.com/common-workflow-language/user_guide/pull/185
  • switch to https://schema.org/version/latest/schema.rdf by @mr-c in https://github.com/common-workflow-language/user_guide/pull/186
  • [ImgBot] Optimize images by @imgbot in https://github.com/common-workflow-language/user_guide/pull/172
  • Introduce both ways of defining arrays by @ktaletsk in https://github.com/common-workflow-language/user_guide/pull/176
  • Swaped hyphen for underscore in link by @longr in https://github.com/common-workflow-language/user_guide/pull/187
  • Create 24conditional-workflow.md by @jjkoehorst in https://github.com/common-workflow-language/userguide/pull/189
  • Update 24conditional-workflow.md by @mr-c in https://github.com/common-workflow-language/userguide/pull/192
  • Fix schema.rdf -> schemaorg-current-http.rdf by @mr-c in https://github.com/common-workflow-language/user_guide/pull/193
  • fix typo by @KushalBeniwal in https://github.com/common-workflow-language/user_guide/pull/194
  • Bump kramdown from 2.3.0 to 2.3.1 by @dependabot in https://github.com/common-workflow-language/user_guide/pull/195
  • Migrate schema from version http and 9.0 to https and latest by @alexiswl in https://github.com/common-workflow-language/user_guide/pull/196
  • Update miscellaneous.md by @medcelerate in https://github.com/common-workflow-language/user_guide/pull/170
  • Bump rexml from 3.2.4 to 3.2.5 by @dependabot in https://github.com/common-workflow-language/user_guide/pull/197
  • Bump addressable from 2.7.0 to 2.8.0 by @dependabot in https://github.com/common-workflow-language/user_guide/pull/198
  • Fix typo (s/it's/its) by @kinow in https://github.com/common-workflow-language/user_guide/pull/204
  • Add missing space between words by @kinow in https://github.com/common-workflow-language/user_guide/pull/199
  • Use backticks for custom-types.yml file name by @kinow in https://github.com/common-workflow-language/user_guide/pull/200
  • Avoid repetition "make use" by @kinow in https://github.com/common-workflow-language/user_guide/pull/201
  • Update interproscan documentation URLs by @kinow in https://github.com/common-workflow-language/user_guide/pull/202
  • Add link to section defining arguments.cwl by @kinow in https://github.com/common-workflow-language/user_guide/pull/203
  • Update Docker image name to match the one configured in arguments.cwl by @neurorepro in https://github.com/common-workflow-language/user_guide/pull/205
  • Update Docker image name in staging lesson to match the one configured in linkfile.cwl by @neurorepro in https://github.com/common-workflow-language/user_guide/pull/206
  • Fixes #177 by @twigleingrid in https://github.com/common-workflow-language/user_guide/pull/208
  • Fix typo in misc by @kinow in https://github.com/common-workflow-language/user_guide/pull/210
  • Correct line number in 19-custom-types.md by @kinow in https://github.com/common-workflow-language/user_guide/pull/212
  • Update the nested worklow description to reflect the content of nestedworkflows.cwl by @neurorepro in https://github.com/common-workflow-language/user_guide/pull/207
  • Specific install instructions by @mr-c in https://github.com/common-workflow-language/user_guide/pull/215
  • Fix SciCrunch link in recommended practices page. by @thetorpedodog in https://github.com/common-workflow-language/user_guide/pull/216
  • fixe yaml indentation in complex example by @emiloslavsky in https://github.com/common-workflow-language/user_guide/pull/221
  • reference correct branch, remove carpentries refs by @mr-c in https://github.com/common-workflow-language/user_guide/pull/223
  • Link to cwl-patterns repo by @mr-c in https://github.com/common-workflow-language/user_guide/pull/225
  • Update index.md by @HenryLiu0 in https://github.com/common-workflow-language/user_guide/pull/230
  • Creating a preview of the outline proposed by @kinow in https://github.com/common-workflow-language/user_guide/pull/226
  • Install graphviz to GitHub Actions by @kinow in https://github.com/common-workflow-language/user_guide/pull/234
  • Remove orphan tag from operations page by @kinow in https://github.com/common-workflow-language/user_guide/pull/236
  • Clarify file names and fix formatting and typos in workflow chapter by @elehcim in https://github.com/common-workflow-language/user_guide/pull/235
  • Fix syntax highlighting and fix output log in workflows.md by @elehcim in https://github.com/common-workflow-language/user_guide/pull/237
  • Separate commands and output by @kinow in https://github.com/common-workflow-language/user_guide/pull/238
  • Update README links to citation and authors files by @kinow in https://github.com/common-workflow-language/user_guide/pull/241
  • Add TypeScript in CWL to tutorials by @kinow in https://github.com/common-workflow-language/user_guide/pull/243
  • Automate generation of outputs by @kinow in https://github.com/common-workflow-language/user_guide/pull/248
  • Make section titles consistent by @kinow in https://github.com/common-workflow-language/user_guide/pull/251
  • Broken link fix by @Smyja in https://github.com/common-workflow-language/user_guide/pull/259
  • Document more features of cwltool by @kinow in https://github.com/common-workflow-language/user_guide/pull/246
  • Add documentation about InlineJavascriptRequirement expressionLib by @kinow in https://github.com/common-workflow-language/user_guide/pull/242
  • Add section about exclusive params with expressions, and emphasize command output lines by @kinow in https://github.com/common-workflow-language/user_guide/pull/247
  • Adjust install instructions by @tetron in https://github.com/common-workflow-language/user_guide/pull/277
  • Typo fix by @Smyja in https://github.com/common-workflow-language/user_guide/pull/273
  • update note content and add windows OS and link to install cwltool by @Fienne in https://github.com/common-workflow-language/user_guide/pull/276
  • fix: change "core concepts" to "topics" by @Fienne in https://github.com/common-workflow-language/user_guide/pull/258
  • Update prerequisites.md by @swzCuroverse in https://github.com/common-workflow-language/user_guide/pull/278
  • feat: add cwl runner source by @Fienne in https://github.com/common-workflow-language/user_guide/pull/263
  • fix broken link by @Fienne in https://github.com/common-workflow-language/user_guide/pull/266
  • Update missing links, edit document by @Fienne in https://github.com/common-workflow-language/user_guide/pull/272
  • Fix emphasize-lines with runcmd by @kinow in https://github.com/common-workflow-language/user_guide/pull/280
  • change concating to concatenating by @Fienne in https://github.com/common-workflow-language/user_guide/pull/285
  • Typo fix by @Smyja in https://github.com/common-workflow-language/user_guide/pull/289
  • Update AUTHORS.md by @swzCuroverse in https://github.com/common-workflow-language/user_guide/pull/283
  • fix typo by @Mackenzie-OO7 in https://github.com/common-workflow-language/user_guide/pull/290
  • Made licensing guideline more neutral in https://github.com/common-workflow-language/user_guide/pull/120
  • fixed broken link by @bamiwoaluko in https://github.com/common-workflow-language/user_guide/pull/274
  • edit typo on home page by @Fienne in https://github.com/common-workflow-language/user_guide/pull/287
  • Fix broken links by @gathoni-k in https://github.com/common-workflow-language/user_guide/pull/291
  • typo fixes & internal link by @tobyhodges in https://github.com/common-workflow-language/user_guide/pull/292
  • Update CONTRIBUTING.md by @swzCuroverse in https://github.com/common-workflow-language/user_guide/pull/293
  • Modified docs by @Mackenzie-OO7 in https://github.com/common-workflow-language/user_guide/pull/295
  • Expand toc nav depth by @gathoni-k in https://github.com/common-workflow-language/user_guide/pull/296
  • Add descriptive link texts by @gathoni-k in https://github.com/common-workflow-language/user_guide/pull/294
  • Update README with current render by @Fienne in https://github.com/common-workflow-language/user_guide/pull/297
  • Better explain how to update the tutorials list by @Fienne in https://github.com/common-workflow-language/user_guide/pull/302
  • add information on which branch to contribute to by @Fienne in https://github.com/common-workflow-language/user_guide/pull/303
  • 2022 Week 41 release by @mr-c in https://github.com/common-workflow-language/user_guide/pull/281

New Contributors

  • @manabuishii made their first contribution in https://github.com/common-workflow-language/user_guide/pull/30
  • @tom-tan made their first contribution in https://github.com/common-workflow-language/user_guide/pull/35
  • @BenjaminHCCarr made their first contribution in https://github.com/common-workflow-language/user_guide/pull/50
  • @hmenager made their first contribution in https://github.com/common-workflow-language/user_guide/pull/65
  • @khillion made their first contribution in https://github.com/common-workflow-language/user_guide/pull/70
  • @sharmatime made their first contribution in https://github.com/common-workflow-language/user_guide/pull/74
  • @jessMaia made their first contribution in https://github.com/common-workflow-language/user_guide/pull/78
  • @rmccole made their first contribution in https://github.com/common-workflow-language/user_guide/pull/79
  • @jirikuncar made their first contribution in https://github.com/common-workflow-language/user_guide/pull/88
  • @zipho made their first contribution in https://github.com/common-workflow-language/user_guide/pull/106
  • @majensen made their first contribution in https://github.com/common-workflow-language/user_guide/pull/111
  • @sersorrel made their first contribution in https://github.com/common-workflow-language/user_guide/pull/112
  • @imgbot made their first contribution in https://github.com/common-workflow-language/user_guide/pull/113
  • @biokcb made their first contribution in https://github.com/common-workflow-language/user_guide/pull/114
  • @alimanfoo made their first contribution in https://github.com/common-workflow-language/user_guide/pull/131
  • @longr made their first contribution in https://github.com/common-workflow-language/user_guide/pull/138
  • @emannuelOC made their first contribution in https://github.com/common-workflow-language/user_guide/pull/145
  • @kinow made their first contribution in https://github.com/common-workflow-language/user_guide/pull/153
  • @tsuchi8 made their first contribution in https://github.com/common-workflow-language/user_guide/pull/147
  • @wgerlach made their first contribution in https://github.com/common-workflow-language/user_guide/pull/169
  • @ktaletsk made their first contribution in https://github.com/common-workflow-language/user_guide/pull/174
  • @stain made their first contribution in https://github.com/common-workflow-language/user_guide/pull/183
  • @jjkoehorst made their first contribution in https://github.com/common-workflow-language/user_guide/pull/185
  • @KushalBeniwal made their first contribution in https://github.com/common-workflow-language/user_guide/pull/194
  • @dependabot made their first contribution in https://github.com/common-workflow-language/user_guide/pull/195
  • @alexiswl made their first contribution in https://github.com/common-workflow-language/user_guide/pull/196
  • @medcelerate made their first contribution in https://github.com/common-workflow-language/user_guide/pull/170
  • @neurorepro made their first contribution in https://github.com/common-workflow-language/user_guide/pull/205
  • @twigleingrid made their first contribution in https://github.com/common-workflow-language/user_guide/pull/208
  • @thetorpedodog made their first contribution in https://github.com/common-workflow-language/user_guide/pull/216
  • @emiloslavsky made their first contribution in https://github.com/common-workflow-language/user_guide/pull/221
  • @HenryLiu0 made their first contribution in https://github.com/common-workflow-language/user_guide/pull/230
  • @elehcim made their first contribution in https://github.com/common-workflow-language/user_guide/pull/235
  • @Smyja made their first contribution in https://github.com/common-workflow-language/user_guide/pull/259
  • @tetron made their first contribution in https://github.com/common-workflow-language/user_guide/pull/277
  • @Fienne made their first contribution in https://github.com/common-workflow-language/user_guide/pull/276
  • @swzCuroverse made their first contribution in https://github.com/common-workflow-language/user_guide/pull/278
  • @Mackenzie-OO7 made their first contribution in https://github.com/common-workflow-language/user_guide/pull/290
  • @bamiwoaluko made their first contribution in https://github.com/common-workflow-language/user_guide/pull/274
  • @gathoni-k made their first contribution in https://github.com/common-workflow-language/user_guide/pull/291

Full Changelog: https://github.com/common-workflow-language/user_guide/compare/v0.3...v0.4

- Common Workflow Language
Published by mr-c over 3 years ago

user_guide - Now with valid metadata!

- Common Workflow Language
Published by mr-c almost 9 years ago

user_guide - Updated metadata

- Common Workflow Language
Published by mr-c almost 9 years ago

user_guide - Initial release

Huge thanks to @tobyhodges for bulk converting from the existing user guide to Carpentry style!

- Common Workflow Language
Published by mr-c almost 9 years ago