diff --git a/.travis.yml b/.travis.yml index 94ba83f5..60b211ad 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,3 +1,7 @@ +sudo: required +services: + - docker + language: python python: - 2.7 diff --git a/_includes/cwl/17-metadata/file-formats.bam b/_includes/cwl/17-metadata/file-formats.bam new file mode 100644 index 00000000..7a3b5102 Binary files /dev/null and b/_includes/cwl/17-metadata/file-formats.bam differ diff --git a/_includes/cwl/17-metadata/sample.yml b/_includes/cwl/17-metadata/sample.yml new file mode 100644 index 00000000..89a41813 --- /dev/null +++ b/_includes/cwl/17-metadata/sample.yml @@ -0,0 +1,7 @@ +aligned_sequences: + 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/conformance-test.yml b/_includes/cwl/conformance-test.yml index 559d38bd..95114735 100644 --- a/_includes/cwl/conformance-test.yml +++ b/_includes/cwl/conformance-test.yml @@ -1,3 +1,18 @@ +# Section 2 +- doc: Test for section 2 + job: 02-1st-example/echo-job.yml + tool: 02-1st-example/1st-tool.cwl + should_fail: false + output: {} + +# Section 3 +- doc: Test for section 3 + job: 03-input/inp-job.yml + tool: 03-input/inp.cwl + should_fail: false + output: {} + +# Section 4 - doc: Test for section 4 job: 04-output/tar-job.yml tool: 04-output/tar.cwl @@ -8,3 +23,161 @@ basename: hello.txt location: Any size: 0 + +# Section 5 +- doc: Test for section 5 + job: 05-stdout/echo-job.yml + tool: 05-stdout/stdout.cwl + output: + output: + class: File + checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b + basename: output.txt + location: Any + size: 13 + +# Section 6 +- doc: Test for section 6 + job: 06-params/tar-param-job.yml + tool: 06-params/tar-param.cwl + output: + example_out: + class: File + checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709 + basename: goodbye.txt + location: Any + size: 0 + +# Section 7 depends on side-effects + +# Section 8 +- doc: Test for section 8 + job: 08-arguments/arguments-job.yml + tool: 08-arguments/arguments.cwl + output: + classfile: + class: File + checksum: sha1$fdb876b40ad9ebc7fee873212e02d5940588642e + basename: Hello.class + location: Any + size: 184 + +# Section 9 depends on side-effects + +# Section 10 +- doc: Test for section 10 + job: 10-array-outputs/array-outputs-job.yml + tool: 10-array-outputs/array-outputs.cwl + output: + output: + - class: File + basename: baz.txt + checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709 + location: Any + size: 0 + - class: File + basename: foo.txt + checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709 + location: Any + size: 0 + +# Section 11 depends on side-effects +# Rest two examples in Section 11 depend on side-effects +- doc: Test for section 11 (1st example) + job: 11-records/record-job1.yml + tool: 11-records/record.cwl + should_fail: true + +# Section 12 depends on side-effects +# Section 13 depends on side-effects +# Section 14 depends on side-effects + +# Section 15 +- doc: Test for section 15 + job: 15-staging/arguments-job.yml + tool: 15-staging/linkfile.cwl + output: + classfile: + class: File + checksum: sha1$fdb876b40ad9ebc7fee873212e02d5940588642e + basename: Hello.class + location: Any + size: 184 + +# Section 16 +# Note: The checksum and size is always changed for every executions +- doc: Test for section 16 + job: 16-file-formats/sample.yml + tool: 16-file-formats/metadata_example.cwl + output: + report: + class: File + basename: output.txt + location: Any + +# Section 17 +# Note: The checksum and size is always changed for every executions +- doc: Test for section 17 (1st example) + job: 17-metadata/sample.yml + tool: 17-metadata/metadata_example2.cwl + output: + report: + class: File + basename: output.txt + location: Any + +- doc: Test for section 17 (extended example) + job: 17-metadata/sample.yml + tool: 17-metadata/metadata_example3.cwl + output: + report: + class: File + basename: output.txt + location: Any + +# Section 19 +# See: Issue #48 +# - doc: Test for section 19 +# job: 19-custom-types/custom-types.yml +# tool: 19-custom-types/costom-types.cwl +# output: +# i5Annotations: +# class: File +# basename: test_proteins.i5_annotations +# location: Any +# size: Any # To be fixed + +# Section 20 +# See: Issue #48 +# - doc: Test for section 20 +# job: 20-software-requirements/custom-types.yml +# tool: 20-software-requirements/costom-types.cwl +# output: +# i5Annotations: +# class: File +# basename: test_proteins.i5_annotations +# location: Any +# size: Any # To be fixed + +# Section 21 +- doc: Test for section 21 + job: 21-1st-workflow/1st-workflow-job.yml + tool: 21-1st-workflow/1st-workflow.cwl + output: + classout: + class: File + checksum: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd + basename: Hello.class + location: Any + size: 419 + +# Section 22 +- doc: Test for section 22 + tool: 22-nested-workflows/nestedworkflows.cwl + output: + classout: + class: File + checksum: sha1$39e3219327347c05aa3e82236f83aa6d77fe6bfd + basename: Hello.class + location: Any + size: 419