v0.4

What's Changed

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

New Contributors

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

Full Changelog: v0.3...v0.4