diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml index f9e234ed0..420f973f8 100644 --- a/v1.0/conformance_test_v1.0.yaml +++ b/v1.0/conformance_test_v1.0.yaml @@ -78,33 +78,33 @@ doc: Test command execution in Docker with stdout redirection - job: v1.0/empty.json - tool: v1.0/egrep-stderr.cwl + tool: v1.0/stderr.cwl doc: Test command line with stderr redirection output: output_file: class: File - checksum: sha1$cec7b8746a78c42060c96505887449bca0142976 - size: 84 + checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15 + size: 4 location: error.txt - job: v1.0/empty.json - tool: v1.0/egrep-stderr-shortcut.cwl + tool: v1.0/stderr-shortcut.cwl doc: Test command line with stderr redirection, brief syntax output: output_file: class: File - checksum: sha1$cec7b8746a78c42060c96505887449bca0142976 - size: 84 + checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15 + size: 4 location: Any - output: output_file: class: File - size: 84 - checksum: sha1$cec7b8746a78c42060c96505887449bca0142976 + size: 4 + checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15 location: std.err job: v1.0/empty.json - tool: v1.0/egrep-stderr-mediumcut.cwl + tool: v1.0/stderr-mediumcut.cwl doc: Test command line with stderr redirection, named brief syntax - job: v1.0/cat-job.json diff --git a/v1.0/v1.0/egrep-stderr-mediumcut.cwl b/v1.0/v1.0/stderr-mediumcut.cwl similarity index 64% rename from v1.0/v1.0/egrep-stderr-mediumcut.cwl rename to v1.0/v1.0/stderr-mediumcut.cwl index ca2732c6f..f04138efc 100644 --- a/v1.0/v1.0/egrep-stderr-mediumcut.cwl +++ b/v1.0/v1.0/stderr-mediumcut.cwl @@ -2,17 +2,12 @@ class: CommandLineTool cwlVersion: v1.0 doc: "Test of capturing stderr output in a docker container." -hints: - DockerRequirement: - dockerPull: debian:wheezy - +requirements: + ShellCommandRequirement: {} inputs: [] - outputs: output_file: type: stderr - -baseCommand: egrep -successCodes: [2] - +arguments: + - { valueFrom: "echo foo 1>&2", shellQuote: False } stderr: std.err diff --git a/v1.0/v1.0/egrep-stderr-shortcut.cwl b/v1.0/v1.0/stderr-shortcut.cwl similarity index 62% rename from v1.0/v1.0/egrep-stderr-shortcut.cwl rename to v1.0/v1.0/stderr-shortcut.cwl index b9088da54..df69badd3 100644 --- a/v1.0/v1.0/egrep-stderr-shortcut.cwl +++ b/v1.0/v1.0/stderr-shortcut.cwl @@ -2,15 +2,11 @@ class: CommandLineTool cwlVersion: v1.0 doc: "Test of capturing stderr output in a docker container." -hints: - DockerRequirement: - dockerPull: debian:wheezy - +requirements: + ShellCommandRequirement: {} inputs: [] - outputs: output_file: type: stderr - -baseCommand: egrep -successCodes: [2] +arguments: + - { valueFrom: "echo foo 1>&2", shellQuote: False } diff --git a/v1.0/v1.0/egrep-stderr.cwl b/v1.0/v1.0/stderr.cwl similarity index 68% rename from v1.0/v1.0/egrep-stderr.cwl rename to v1.0/v1.0/stderr.cwl index d7a8814b9..1ec5f289b 100644 --- a/v1.0/v1.0/egrep-stderr.cwl +++ b/v1.0/v1.0/stderr.cwl @@ -2,14 +2,13 @@ class: CommandLineTool cwlVersion: v1.0 doc: "Test of capturing stderr output in a docker container." -hints: - DockerRequirement: - dockerPull: debian:wheezy +requirements: + ShellCommandRequirement: {} inputs: [] outputs: output_file: type: File outputBinding: {glob: error.txt} -baseCommand: egrep -successCodes: [2] +arguments: + - { valueFrom: "echo foo 1>&2", shellQuote: False } stderr: error.txt diff --git a/v1.1.0-dev1/CommandLineTool.yml b/v1.1.0-dev1/CommandLineTool.yml index d98f85a1d..bbf0d33e5 100644 --- a/v1.1.0-dev1/CommandLineTool.yml +++ b/v1.1.0-dev1/CommandLineTool.yml @@ -747,7 +747,6 @@ $graph: - name: package type: string doc: "The common name of the software to be configured." - jsonldPredicate: "@id" - name: version type: string[]? doc: "The (optional) version of the software to configured." diff --git a/v1.1.0-dev1/Process.yml b/v1.1.0-dev1/Process.yml index cf8e03aed..cca9abe30 100644 --- a/v1.1.0-dev1/Process.yml +++ b/v1.1.0-dev1/Process.yml @@ -595,7 +595,6 @@ $graph: doc: | Specify valid types of data that may be assigned to this parameter. - - name: OutputParameter type: record extends: Parameter diff --git a/v1.1.0-dev1/UserGuide.yml b/v1.1.0-dev1/UserGuide.yml index 025571073..95688ce51 100644 --- a/v1.1.0-dev1/UserGuide.yml +++ b/v1.1.0-dev1/UserGuide.yml @@ -183,7 +183,7 @@ The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not - abosolute. As a result, positions do not have to be sequential, three + absolute. As a result, positions do not have to be sequential, three parameters with positions `[1, 3, 5]` will result in the same command line as `[1, 2, 3]`. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself @@ -290,8 +290,8 @@ - | ## Parameter references - In a previous example, we used extracted a file using the "tar" program. - However, that example was very limited becuase it assumed that the file + In a previous example, we extracted a file using the "tar" program. + However, that example was very limited because it assumed that the file we were interested in was called "hello.txt". In this example, you will see how to reference the value of input parameters dynamically from other fields. @@ -356,7 +356,7 @@ containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output - files can be recovered from the contianer. CWL can perform this work + files can be recovered from the container. CWL can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers. @@ -466,7 +466,7 @@ tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, - `$(runtime.ram)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See + `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment](CommandLineTool.html#Runtime_environment) section of the CWL specification for details. @@ -522,7 +522,7 @@ - | ``` - *array-outpust-job.yml* + *array-outputs-job.yml* ``` - $include: examples/array-outputs-job.yml - | @@ -662,6 +662,16 @@ - | ``` + As this tool does not require any `inputs` we can run it with an (almost) empty job file: + + *empty.yml* + ``` + {} + | + ``` + + We can then run `expression.cwl`: + ``` $ cwl-runner expression.cwl empty.yml [job 140000594593168] /home/example$ echo -A 2 -B baz -C 10 9 8 7 6 5 4 3 2 1 @@ -796,7 +806,7 @@ class: Workflow ``` - The 'cwlVersion` field indicates the version of the CWL spec used by the + The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow. @@ -820,7 +830,7 @@ The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier - and a data type. The `source` connects the output parameter `classfile` + and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `classout`. ``` diff --git a/v1.1.0-dev1/concepts.md b/v1.1.0-dev1/concepts.md index d3eac2364..c1a9ced8d 100644 --- a/v1.1.0-dev1/concepts.md +++ b/v1.1.0-dev1/concepts.md @@ -89,7 +89,7 @@ preprocessing steps described in the [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html). An implementation may formally validate the structure of a CWL document using SALAD schemas located at -https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-4 +https://github.com/common-workflow-language/common-workflow-language/tree/master/v1.1.0-dev1 ## Identifiers diff --git a/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml b/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml index 640c062d9..ec8c2fe2e 100644 --- a/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml +++ b/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml @@ -77,34 +77,34 @@ tool: v1.1.0-dev1/cat3-tool-mediumcut.cwl doc: Test command execution in Docker with stdout redirection -- job: - tool: v1.1.0-dev1/egrep-stderr.cwl +- job: v1.1.0-dev1/empty.json + tool: v1.1.0-dev1/stderr.cwl doc: Test command line with stderr redirection output: output_file: class: File - checksum: sha1$cec7b8746a78c42060c96505887449bca0142976 - size: 84 + checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15 + size: 4 location: error.txt -- job: - tool: v1.1.0-dev1/egrep-stderr-shortcut.cwl +- job: v1.1.0-dev1/empty.json + tool: v1.1.0-dev1/stderr-shortcut.cwl doc: Test command line with stderr redirection, brief syntax output: output_file: class: File - checksum: sha1$cec7b8746a78c42060c96505887449bca0142976 - size: 84 + checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15 + size: 4 location: Any - output: output_file: class: File - size: 84 - checksum: sha1$cec7b8746a78c42060c96505887449bca0142976 + size: 4 + checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15 location: std.err - job: - tool: v1.1.0-dev1/egrep-stderr-mediumcut.cwl + job: v1.1.0-dev1/empty.json + tool: v1.1.0-dev1/stderr-mediumcut.cwl doc: Test command line with stderr redirection, named brief syntax - job: v1.1.0-dev1/cat-job.json @@ -173,17 +173,6 @@ tool: v1.1.0-dev1/wc-tool.cwl doc: Test command execution in with stdin and stdout redirection -- job: v1.1.0-dev1/wc-job.json - output: - output: - class: File - checksum: sha1$631bfbac524e2d04cdcc5ec33ade827fc10b06ae - location: output - size: 15 - tool: v1.1.0-dev1/wc-tool-shortcut.cwl - doc: Test command execution in with stdin and stdout redirection using stdin shortcut - - - job: v1.1.0-dev1/parseInt-job.json output: {output: 42} tool: v1.1.0-dev1/parseInt-tool.cwl @@ -309,6 +298,16 @@ tool: v1.1.0-dev1/env-wf2.cwl doc: Test requirements override hints +- job: v1.1.0-dev1/env-job.json + output: + out: + class: File + checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6 + location: out + size: 9 + tool: v1.1.0-dev1/env-wf3.cwl + doc: Test requirements on workflow steps + - job: v1.1.0-dev1/empty.json output: {count_output: 16} tool: v1.1.0-dev1/count-lines9-wf.cwl @@ -671,7 +670,23 @@ } } tool: v1.1.0-dev1/test-cwl-out.cwl - doc: Test support for reading cwl.output.json when running in Docker container + doc: | + Test support for reading cwl.output.json when running in a Docker container + and just 'path' is provided. + +- job: v1.1.0-dev1/empty.json + output: { + "foo": { + "location": "foo", + "class": "File", + "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15", + "size": 4 + } + } + tool: v1.1.0-dev1/test-cwl-out2.cwl + doc: | + Test support for reading cwl.output.json when running in a Docker container + and just 'location' is provided. - job: v1.1.0-dev1/abc.json output: @@ -785,10 +800,10 @@ - job: v1.1.0-dev1/dir4-job.yml output: { "outlist": { - "checksum": "sha1$2ab6f189e84753c05a23413fbf6b6fbf4c53489f", - "size": 90, - "location": "output.txt", - "class": "File" + "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592", + "size": 20, + "location": "output.txt", + "class": "File" } } tool: v1.1.0-dev1/dir4.cwl @@ -905,3 +920,75 @@ "size": 12010 tool: v1.1.0-dev1/initialworkdirrequirement-docker-out.cwl doc: Test output of InitialWorkDir + +- job: v1.1.0-dev1/wc-job.json + output: {count_output: 16} + tool: v1.1.0-dev1/count-lines10-wf.cwl + doc: Test embedded subworkflow + +- job: v1.1.0-dev1/docker-array-secondaryfiles-job.json + output: { + "bai_list": { + "checksum": "sha1$081fc0e57d6efa5f75eeb237aab1d04031132be6", + "location": "fai.list", + "class": "File", + "size": 386 + } + } + tool: v1.1.0-dev1/docker-array-secondaryfiles.cwl + doc: Test secondaryFiles on array of files. + +- job: v1.1.0-dev1/dir7.yml + output: { + "dir": { + "location": "a_directory", + "class": "Directory", + "listing": [ + { + "class": "File", + "location": "whale.txt", + "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376", + "size": 1111 + }, + { + "class": "File", + "location": "hello.txt", + "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b", + "size": 13 + } + ] + } + } + tool: v1.1.0-dev1/dir7.cwl + doc: Test directory literal output created by ExpressionTool + +- job: v1.1.0-dev1/empty.json + output: + lit: + location: "a_file" + class: "File" + checksum: "sha1$fea23663b9c8ed71968f86415b5ec091bb111448" + size: 19 + tool: v1.1.0-dev1/file-literal-ex.cwl + doc: Test file literal output created by ExpressionTool + +- job: v1.1.0-dev1/empty.json + output: + "thing": { + "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", + "location": "thing", + "class": "File", + "size": 0 + } + tool: v1.1.0-dev1/docker-output-dir.cwl + doc: Test dockerOutputDirectory + +- job: v1.1.0-dev1/empty.json + output: + out: + class: File + checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519 + location: out + size: 15 + tool: v1.1.0-dev1/imported-hint.cwl + doc: Test hints with $import diff --git a/v1.1.0-dev1/examples/arguments.cwl b/v1.1.0-dev1/examples/arguments.cwl index 03057b0c9..385a6665c 100644 --- a/v1.1.0-dev1/examples/arguments.cwl +++ b/v1.1.0-dev1/examples/arguments.cwl @@ -1,7 +1,6 @@ cwlVersion: v1.1.0-dev1 class: CommandLineTool label: Example trivial wrapper for Java 7 compiler -baseCommand: javac hints: DockerRequirement: dockerPull: java:7 diff --git a/v1.1.0-dev1/examples/empty.json b/v1.1.0-dev1/examples/empty.json new file mode 100644 index 000000000..0967ef424 --- /dev/null +++ b/v1.1.0-dev1/examples/empty.json @@ -0,0 +1 @@ +{} diff --git a/v1.1.0-dev1/examples/nestedworkflows.cwl b/v1.1.0-dev1/examples/nestedworkflows.cwl new file mode 100644 index 000000000..3963109e6 --- /dev/null +++ b/v1.1.0-dev1/examples/nestedworkflows.cwl @@ -0,0 +1,52 @@ +cwlVersion: v1.0 +class: Workflow + +inputs: [] + +outputs: + classout: + type: File + outputSource: compile/classout + +requirements: + - class: SubworkflowFeatureRequirement + +steps: + compile: + run: 1st-workflow.cwl + in: + inp: + source: create-tar/tar + ex: + default: "Hello.java" + out: [classout] + + create-tar: + requirements: + - class: InitialWorkDirRequirement + listing: + - entryname: Hello.java + entry: | + public class Hello { + public static void main(String[] argv) { + System.out.println("Hello from Java"); + } + } + in: [] + out: [tar] + run: + class: CommandLineTool + requirements: + - class: ShellCommandRequirement + arguments: + - shellQuote: false + valueFrom: | + date + tar cf hello.tar Hello.java + date + inputs: [] + outputs: + tar: + type: File + outputBinding: + glob: "hello.tar" diff --git a/v1.1.0-dev1/v1.1.0-dev1/binding-test.cwl b/v1.1.0-dev1/v1.1.0-dev1/binding-test.cwl index 68cdc03a4..66a74b8b9 100755 --- a/v1.1.0-dev1/v1.1.0-dev1/binding-test.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/binding-test.cwl @@ -23,7 +23,8 @@ inputs: inputBinding: position: -1 -outputs: [] +outputs: + args: string[] baseCommand: python arguments: ["bwa", "mem"] diff --git a/v1.1.0-dev1/v1.1.0-dev1/cat1-testcli.cwl b/v1.1.0-dev1/v1.1.0-dev1/cat1-testcli.cwl index 5fe8748d2..aa40435c9 100755 --- a/v1.1.0-dev1/v1.1.0-dev1/cat1-testcli.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/cat1-testcli.cwl @@ -29,7 +29,7 @@ } } ], - "outputs": [], + "outputs": [{"id": "args", "type": "string[]"}], "baseCommand": "python", "arguments": ["cat"] } diff --git a/v1.1.0-dev1/v1.1.0-dev1/cat5-tool.cwl b/v1.1.0-dev1/v1.1.0-dev1/cat5-tool.cwl index 5b081f7f2..6125644f9 100755 --- a/v1.1.0-dev1/v1.1.0-dev1/cat5-tool.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/cat5-tool.cwl @@ -1,11 +1,13 @@ #!/usr/bin/env cwl-runner +$namespaces: + ex: http://example.com/ cwlVersion: v1.1.0-dev1 class: CommandLineTool doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: dockerPull: "debian:wheezy" - BlibberBlubberFakeRequirement: + ex:BlibberBlubberFakeRequirement: fakeField: fraggleFroogle inputs: file1: diff --git a/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl b/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl new file mode 100755 index 000000000..5714cd913 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl @@ -0,0 +1,22 @@ +#!/usr/bin/env cwl-runner +class: Workflow +cwlVersion: v1.1.0-dev1 +inputs: + file1: File +outputs: + count_output: {type: int, outputSource: step1/count_output} +requirements: + SubworkflowFeatureRequirement: {} +steps: + step1: + in: {file1: file1} + out: [count_output] + run: + class: Workflow + inputs: + file1: File + outputs: + count_output: {type: int, outputSource: step2/output} + steps: + step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]} + step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]} diff --git a/v1.1.0-dev1/v1.1.0-dev1/dir4.cwl b/v1.1.0-dev1/v1.1.0-dev1/dir4.cwl index 0bca5f5b8..26f63c1fd 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/dir4.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/dir4.cwl @@ -9,9 +9,9 @@ outputs: type: File outputBinding: glob: output.txt -arguments: ["cd", "$(inputs.inf.dirname)", +arguments: ["cd", "$(inputs.inf.dirname)/xtestdir", {shellQuote: false, valueFrom: "&&"}, "find", ".", {shellQuote: false, valueFrom: "|"}, "sort"] -stdout: output.txt \ No newline at end of file +stdout: output.txt diff --git a/v1.1.0-dev1/v1.1.0-dev1/dir5.cwl b/v1.1.0-dev1/v1.1.0-dev1/dir5.cwl index 7eaa481a1..177d98172 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/dir5.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/dir5.cwl @@ -11,7 +11,7 @@ outputs: type: File outputBinding: glob: output.txt -arguments: ["find", ".", +arguments: ["find", "-L", ".", {shellQuote: false, valueFrom: "|"}, "sort"] stdout: output.txt \ No newline at end of file diff --git a/v1.1.0-dev1/v1.1.0-dev1/dir7.cwl b/v1.1.0-dev1/v1.1.0-dev1/dir7.cwl new file mode 100644 index 000000000..b5a43a00b --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/dir7.cwl @@ -0,0 +1,12 @@ +class: ExpressionTool +cwlVersion: v1.1.0-dev1 +requirements: + InlineJavascriptRequirement: {} +inputs: + files: File[] +outputs: + dir: Directory +expression: | + ${ + return {"dir": {"class": "Directory", "basename": "a_directory", "listing": inputs.files}}; + } \ No newline at end of file diff --git a/v1.1.0-dev1/v1.1.0-dev1/dir7.yml b/v1.1.0-dev1/v1.1.0-dev1/dir7.yml new file mode 100644 index 000000000..7ad068585 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/dir7.yml @@ -0,0 +1,5 @@ +files: + - class: File + location: hello.txt + - class: File + location: whale.txt diff --git a/v1.1.0-dev1/v1.1.0-dev1/docker-array-secondaryfiles-job.json b/v1.1.0-dev1/v1.1.0-dev1/docker-array-secondaryfiles-job.json new file mode 100644 index 000000000..5d178fc63 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/docker-array-secondaryfiles-job.json @@ -0,0 +1,12 @@ +{ + "fasta_path": [ + { + "class": "File", + "location": "ref.fasta" + }, + { + "class": "File", + "location": "ref2.fasta" + } + ] +} diff --git a/v1.1.0-dev1/v1.1.0-dev1/docker-array-secondaryfiles.cwl b/v1.1.0-dev1/v1.1.0-dev1/docker-array-secondaryfiles.cwl new file mode 100644 index 000000000..8fedb9eda --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/docker-array-secondaryfiles.cwl @@ -0,0 +1,38 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.1.0-dev1 + +requirements: + - class: DockerRequirement + dockerPull: debian:8 + - class: InlineJavascriptRequirement + - class: ShellCommandRequirement + +class: CommandLineTool + +inputs: + fasta_path: + type: + type: array + items: File + secondaryFiles: + - .fai + +outputs: + bai_list: + type: File + outputBinding: + glob: "fai.list" + +arguments: + - valueFrom: ${ + var fai_list = ""; + for (var i = 0; i < inputs.fasta_path.length; i ++) { + fai_list += " cat " + inputs.fasta_path[i].path +".fai" + " >> fai.list && " + } + return fai_list.slice(0,-3) + } + position: 1 + shellQuote: false + +baseCommand: [] diff --git a/v1.1.0-dev1/v1.1.0-dev1/docker-output-dir.cwl b/v1.1.0-dev1/v1.1.0-dev1/docker-output-dir.cwl new file mode 100644 index 000000000..e50e1d5f2 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/docker-output-dir.cwl @@ -0,0 +1,13 @@ +class: CommandLineTool +cwlVersion: v1.1.0-dev1 +requirements: + DockerRequirement: + dockerPull: debian:8 + dockerOutputDirectory: /other +inputs: [] +outputs: + thing: + type: File + outputBinding: + glob: thing +baseCommand: ["touch", "/other/thing"] diff --git a/v1.1.0-dev1/v1.1.0-dev1/env-wf1.cwl b/v1.1.0-dev1/v1.1.0-dev1/env-wf1.cwl index df382e2bb..a8678459c 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/env-wf1.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/env-wf1.cwl @@ -11,8 +11,7 @@ outputs: outputSource: step1/out requirements: - - class: SubworkflowFeatureRequirement - - class: EnvVarRequirement + EnvVarRequirement: envDef: TEST_ENV: override diff --git a/v1.1.0-dev1/v1.1.0-dev1/env-wf2.cwl b/v1.1.0-dev1/v1.1.0-dev1/env-wf2.cwl index 1547e924b..dad9d9554 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/env-wf2.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/env-wf2.cwl @@ -11,8 +11,7 @@ outputs: outputSource: step1/out requirements: - - class: SubworkflowFeatureRequirement - - class: EnvVarRequirement + EnvVarRequirement: envDef: TEST_ENV: override diff --git a/v1.1.0-dev1/v1.1.0-dev1/env-wf3.cwl b/v1.1.0-dev1/v1.1.0-dev1/env-wf3.cwl new file mode 100644 index 000000000..90f57df04 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/env-wf3.cwl @@ -0,0 +1,22 @@ +#!/usr/bin/env cwl-runner +class: Workflow +cwlVersion: v1.1.0-dev1 + +inputs: + in: string + +outputs: + out: + type: File + outputSource: step1/out + +steps: + step1: + run: env-tool2.cwl + requirements: + EnvVarRequirement: + envDef: + TEST_ENV: override + in: + in: in + out: [out] diff --git a/v1.1.0-dev1/v1.1.0-dev1/envvar.yml b/v1.1.0-dev1/v1.1.0-dev1/envvar.yml new file mode 100644 index 000000000..097c3f27d --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/envvar.yml @@ -0,0 +1,4 @@ +class: EnvVarRequirement +envDef: + - envName: "TEST_ENV" + envValue: "hello test env" diff --git a/v1.1.0-dev1/v1.1.0-dev1/file-literal-ex.cwl b/v1.1.0-dev1/v1.1.0-dev1/file-literal-ex.cwl new file mode 100644 index 000000000..7d1912f85 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/file-literal-ex.cwl @@ -0,0 +1,11 @@ +class: ExpressionTool +cwlVersion: v1.1.0-dev1 +requirements: + InlineJavascriptRequirement: {} +inputs: [] +outputs: + lit: File +expression: | + ${ + return {"lit": {"class": "File", "basename": "a_file", "contents": "Hello file literal."}}; + } \ No newline at end of file diff --git a/v1.1.0-dev1/v1.1.0-dev1/imported-hint.cwl b/v1.1.0-dev1/v1.1.0-dev1/imported-hint.cwl new file mode 100755 index 000000000..b6fe82fa1 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/imported-hint.cwl @@ -0,0 +1,13 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.1.0-dev1 +class: CommandLineTool +inputs: [] +outputs: + out: stdout + +hints: +- $import: envvar.yml + +baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"] + +stdout: out diff --git a/v1.1.0-dev1/v1.1.0-dev1/ref.fasta.fai b/v1.1.0-dev1/v1.1.0-dev1/ref.fasta.fai new file mode 100644 index 000000000..e5d66331d --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/ref.fasta.fai @@ -0,0 +1,5 @@ +0$chr1$9001$11468 2567 19 2567 2568 +1$chr1$53713$55817 2204 2607 2204 2205 +2$chr1$65161$67630 2569 4832 2569 2570 +3$chr1$82792$85041 2349 7422 2349 2350 +4$chr1$98000$100116 2216 9793 2216 2217 diff --git a/v1.1.0-dev1/v1.1.0-dev1/ref2.fasta b/v1.1.0-dev1/v1.1.0-dev1/ref2.fasta new file mode 100644 index 000000000..bad272557 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/ref2.fasta @@ -0,0 +1,10 @@ +>0$chr1$9001$11468 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTCGCGGTACCCTCAGCCGGCCCGCCCGCCCGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGACAACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCCGTTGCAAAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGACACATGCTAGCGCGTCGGGGTGGAGGCGTGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGACACATGCTACCGCGTCCAGGGGTGGAGGCGTGGCGCAGGCGCAGAGAGGCGCACCGCGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGTGGAGGCGTGGCGCAGGCGCAGAGACGCAAGCCTACGGGCGGGGGTTGGGGGGGCGTGTGTTGCAGGAGCAAAGTCGCACGGCGCCGGGCTGGGGCGGGGGGAGGGTGGCGCCGTGCACGCGCAGAAACTCACGTCACGGTGGCGCGGCGCAGAGACGGGTAGAACCTCAGTAATCCGAAAAGCCGGGATCGACCGCCCCTTGCTTGCAGCCGGGCACTACAGGACCCGCTTGCTCACGGTGCTGTGCCAGGGCGCCCCCTGCTGGCGACTAGGGCAACTGCAGGGCTCTCTTGCTTAGAGTGGTGGCCAGCGCCCCCTGCTGGCGCCGGGGCACTGCAGGGCCCTCTTGCTTACTGTATAGTGGTGGCACGCCGCCTGCTGGCAGCTAGGGACATTGCAGGGTCCTCTTGCTCAAGGTGTAGTGGCAGCACGCCCACCTGCTGGCAGCTGGGGACACTGCCGGGCCCTCTTGCTCCAACAGTACTGGCGGATTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>1$chr1$53713$55817 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATAGATGGAATAAATAAAATGTGAACTTAGGTAAATTATAAATTAATAAAGTATATTTTTAAAATTTCCATTTTAATTTCTGTTTAAATTAGAATAAGAAACAAAAACAACTATGTAATACGTGTGCAAAGCCCTGAACTGAGATTTGACTTTACCTTGAGCTTTGTCAGTTTACGATGCTATTTCAGTTTTGTGCTCAGATTTGAGTGATTGCAGGAAGAGAATAAATTTCTTTAATGCTGTCAAGACTTTAAATAGATACAGACAGAGCATTTTCACTTTTTCCTACATCTCTATTATTCTAAAAATGAGAACATTCCAAAAGTCAACCATCCAAGTTTATTCTAAATAGATGTGTAGAAATAACAGTTGTTTCACAGGAGACTAATCGCCCAAGGATATGTGTTTAGAGGTACTGGTTTCTTAAATAAGGTTTTCTAGTCAGGCAAAAGATTCCCTGGAGCTTATGCATCTGTGGTTGATATTTTGGGATAAGAATAAAGCTAGAAATGGTGAGGCATATTCAATTTCATTGAAGATTTCTGCATTCAAAATAAAAACTCTATTGAAGTTACACATACTTTTTTCATGTATTTGTTTCTACTGCTTTGTAAATTATAACAGCTCAATTAAGAGAAACCGTACCTATGCTATTTTGTCCTGTGATTCTCCAAGAACCTTCCTAAGTTATTCTACTTAATTGCTTTATCACTCATATGAATGGGAATTTCTTCTCTTAATTGCTGCTAATCTCCCCCATCTTCAAATACTCTACCGGGCTTCTGGAACACCACAGCTTCCTGGCTTTTTCTCCTACCTCCTGGGCAAGTCCTTCCCTGTGTCTTTTGTTGAGTGTTCCTCATCTGCTTAACTACCAATCAACCTATTGCCCCTAATTTGATCTTTGGCCTGTTTTCACTTAGATTCTATCCCTACGTATCACCCATTCCCACAGCTTTAATCACCATCTAAACACTAGGGGCTCTCAAACCTTGTATTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTCCTTTTCTTTCCTTTTCTTTCTTTCATTCTTTCTTTCTTTTTTAAGGGGCAGGGTCTCACTATGTTGCTGAGGCTGGTCTCAAACTCCTGACCTCAAGCAATCTGTCTGCTTCAGCCTCCCAAGTAGCTGAGAATACAGGGACAAGCCATTGCACCTGACCCTGGTACTATTTCTTGAGTTCCTGATCCACAGATCTAACCTCCTACTTTCCTGGATGCCACACAAGATCTTCCACTCAACAAGTCTGCAACTAAACTAGCCTTCCTCTTTTCAAACCTACTCTTCTTTCAGTGTTCTCAGTCACAATAATTTGTACCAACTAGTTACCTAGTTGCACAACCCAAAATCTGGGAAAAATAATAGATTTCTTTCTCCATAGTACCCCCAAATCAATAAATCATCAAGTCTTATTCTACCTTCCAAAGAGCCTTACATATGTTCCTTTATTTTCATCTGTAACACCACTATTCCTGTCTAAGCCTACCTATGTCATTTTTGGAAGAGAATATAGTCACCTATGCGACCTTCCCACTTAAAATCCTACTATTTACGCTTCAGTAAAAGAAAAAAAATTTTTAATCTAAGTATGTAATTCTTTTGCTGAAGACACTTCACTTGCTTCTGTGCCCTTAAACTGGTATGTTATCATGGTATAGTAGGCCATCCAAGACCTGGCTTCCTTCCTTTTTTTCAGTCTCAGAGAATAACATACTCTTTCCCTGCAACTCCAGATCCAATTTGGTTTTCTTTTACTTGCCTGGAAACTCCAAAATCTATCAACTCTGGGGCTTTCCACTAGCTAATCATTTTGTATACAATATTTGTCCTTCATGTTTTGCCTCTTAACATCTCAGCTTTCAGTTTCATCATTTTACCAGGGAGGCCTCCCAGAACCTGAGTCCAGAAGAGTTCCTTCCATTGTATATTCCTCTAGCACTACCTATTACCTCTTTTGTAAGACTAACAGCCCTCAAAATTTTTCATTCAGTGATGTCTTCCTCATTGCATTTTAAGTTCAACATGAGCAGGACTTTGTCGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>2$chr1$65161$67630 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAATCGAAGCATTATTACTTACTCTCTTGTTAACCTATCTGGATTTTAATTTTGTAACTTTATTATATTTGTTTTGCTGTGATTCTTTAAAAAGCACCTTTAGACTCAGTGAGATAGCAAAAATATCCAAATAGGCCAAAAAATTGTGGCAATGTCCTCTCACTCAGGAAAATTCTGTGTGTTTTCTCTAATGGCCAAGGGAAAACTTGTGAGACTATAAAAGTTAGTCTCAGTACACAAAGCTCAGACTGGCTATTCCCAGATCTCTTCAGGTACATCTAGTCCATTCATAAAGGGCTTTTAATTAACCAAGTGGTTTACTAAAAAGGACAATTCACTACATATTATTCTCTTACAGTTTTTATGCCTCATTCTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAGGTGGAAACAAAGACAAAACACATATATTAGAAGAATGAATGAAATTGTAGCATTTTATTGACAATGAGATGGTTCTATTAGTAGGAATCTATTCTGCATAATTCCATTTTGTGTTTACCTTCTGGAAAAATGAAAGGATTCTGTATGGTTAACTTAAATACTTAGAGAAATTAATATGAATAATGTTAGCAAGAATAACCCTTGTTATAAGTATTATGCTGGCAACAATTGTCGAGTCCTCCTCCTCACTCTTCTGGGCTAATTTGTTCTTTTCTCCCCATTTAATAGTCCTTTTCCCCATCTTTCCCCAGGTCCGGTGTTTTCTTACCCACCTCCTTCCCTCCTTTTTATAATACCAGTGAAACTTGGTTTGGAGCATTTCTTTCACATAAAGGTACAAATCATACTGCTAGAGTTGTGAGGATTTTTACAGCTTTTGAAAGAATAAACTCATTTTAAAAACAGGAAAGCTAAGGCCCAGAGATTTTTAAATGATATTCCCATGATCACACTGTGAATTTGTGCCAGAACCCAAATGCCTACTCCCATCTCACTGAGACTTACTATAAGGACATAAGGCATTTATATATATATATATTATATATACTATATATTTATATATATTACATATTATATATATAATATATATTATATAATATATATTATATTATATAATATATAATATAAATATAATATAAATTATATTATATAATATATAATATAAATATAATATAAATTATATAAATATAATATATATTTTATTATATAATATAATATATATTATATAAATATAATATATAAATTATATAATATAATATATATTATATAATATAATATATTTTATTATATAAATATATATTATATTATATAATATATATTTTATTATATAATATATATTATATATTTATAGAATATAATATATATTTTATTATATAATATATATTATATAATATATATTATATTTATATATAACATATATTATTATATAAAATATGTATAATATATATTATATAAATATATTTATATATTATATAAATATATATATTATATATAATTCTAATGGTTGAATTCCAAGAATAATCTATGGCATGAAAGATTTTACCTGTCAACAGTGGCTGGCTCTTCATGGTTGCTACAATGAGTGTGTAAGATTCTGAAGGACTCCTTTAATAAGCCTAAACTTAATGTTCAACTTAGAATAAATACAATTCTTCTAATTTTTTTTGAATAATTTTTAAAAAGTCAGAAATGAGCTTTGAAAGAATTATGGTGGTGAAGGATCCCCTCAGCAGCACAAATTCAGGAGAGAGATGTCTTAACTACGTTAGCAAGAAATTCCTTTTGCTAAAGAATAGCATTCCTGAATTCTTACTAACAGCCATGATAGAAAGTCTTTTGCTACAGATGAGAACCCTCGGGTCAACCTCATCCTTGGCATATTTCATGTGAAGATATAACTTCAAGATTGTCCTTGCCTATCAATGAAATGAATTAATTTTATGTCAATGCATATTTAAGGTCTATTCTAAATTGCACACTTTGATTCAAAAGAAACAGTCCAACCAACCAGTCAGGACAGAAATTATCTCACAATAAAAATCCTATCGTTTGTACTGTCAATGATTAGTATGATTATATTTATTACCGTGCTAAGCAGAAGAGAAATGAAGTGAATGTTCATGATTTATTCCACTATTAGACTTCTCTTTATTCTTAAAAATATTTAAGATCACTAAATTTTTATAGGACTTTAAAAACAGTAATGTGCTGCTTTGAGTGTGTAGGACTAAGAAATGGGATTCAGAGTAGTAAAGAGAAAAGTGGAATTTCCAAGCACTATGAATTACTGTTCTTTAAAAAACAGCAAAAATCAAATAACAGTATTCCTCCAAAAAAGATGGCAAGTGTAAACTCTATACCTTCATGTCTCCCGTGGAATGTTAGTGATCAATTTCCACTTCTCTCTTTTACATCTTACTTGCCCATTAACTCTTATACCTAATCCAAAGATTGTTAATATGGCTATGTCTCACTTTCAGGACACCTTTTATTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>3$chr1$82792$85041 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+>4$chr1$98000$100116 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCATGACAGGCAGAGCTCCCTGTTGAGCCACAGAGATTTAGAGAATGGCTGTTAACACAGCATAATCCAGCCCATCCTGACTAATCTGATATTAACATGTATAATAAAGAATTCTATCAATGCTGAGGGAAGATGACTAGTTAAGGTCCTAGGTTGCAAGTCTCAAAACCTCTTCTAAGGATTGTAGACAGGAAATTAAATGACTTCTAGTCCCTAGAGTTCCCAATCTCCTACCATCCCATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAAACCAGAGCTTCCCTCAGAACCCTTAGCCTGCCAGATGGCTTCTTGGAGAGCCCTCACTCACTTTTCTCCTTCTGCTATTGCTGCTCATTCATTCCAGTTTTTAAAAATTCATCTTTATCCAGGAACCTCGCTTCTAGAAAAGTCATACAGGTGCTTCCAGGAGGCTACATGGGCACCCATATTTTTCTAGCCACTTTCATTAGACCAATGCAGCAGAGAAGAAAAGCCTCAATAATTATTATGACATGGCATGTTAGGATACCAAGTAAATTGCATTTGTAAAATGTGATTTTCTGTTGGTGTTCACTTCAGCTCTACTGACATTTGGTAAGTATTATTGACTGACTGACTAACTAATGTGGTCATTAGTCTTCATAAAGAAAGGCTCTCTACAAAAACGGAGGGATGCCCTTTTTCTGGCATTTAATACGTAAGAAATTGCCTCCAATAGAAACCAGAGTTGCCTGATTACTATCAGCACAGGAGAAATGTATTAATGTGCCTTTCTAGTAACAGGTTTTTAGAAAGTCAAATATAAACAAATCTGTCTATTTGTGTGTGTGCATGTGGTAGTGGGGAGGGAAGAAAAAAGGAGGGGGAGAGAAAGAGAAATAAGAACCAAGTTTATTATACTGTATTCAGGGGGAAAAAATTTTCCCAAGGTCCTAACAGAAGAGCAAAGTGCCACTGTCAATAGCCTCAGTAGTGTTAGGGTTGCTTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTTCCTTTTTTTTCTTTCTCTTTTTTTCTTCTTTTTTTTTTCTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTGGACAGAGTCTCACACTGTCACCTGGGCTGGAGTGCATTGGTGCAATCTCGACTCACTGCAACTTCTGCCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCGCCCAAGTAGCTGGGATTACAGGTGTCTGCCACCGTGCCTAGCTAATTTTTTTGTATTTTTAGTAGAGATGAGGTTTCACTATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCATGATCCACCCACGTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCCCCTGGCCAGGATTGCTTTTACAGCCAGTCTTCAGGTGCCCACTGTAGGAACAATGTCATTTAACCCTCGGGATTATTCTGTGCCAAATATGGATAATGACTAATATCCAACACAGATATTCTCAGCTCAGAAGAGCAATTAGCAAATTCATAAATTAAGTGCTTGCTTCCTCTTTAGTCAAATACAAACGTTTGTTAAAAGATATTATTTTGCTTTACACTTTTTCTCTCAGAAATAAGCAGATGCTTGAATTCCCACAGTGCTGCTTGAGCCTCACACCATGTCATCCTGCCAGGCACCCAGATCCAGTTCTAGAGTTTCACATGATCGTGAGTGTTGGTTAATAAGTCAATGTGAACTGGGAGGGGAGATTTTTCAGGAGTGCCACAGGGCTCTCCCTTTAATCACATACACTCCCTGCTTTCATTGGAAAGTGTATAATGATGTCAGAGTGCCCCAGAATGGAGCTAGTTGGAAGACTGCCGTCATAGGGATGCCTTAGTGAATTAATAAGGTTTTAATTTCTGGCTCTCAACTTTGTAGATGTAAAAGTTGATTTATCAATATGTGAGAAAGGATGAATCTTTCTGAAGGTTATGTCATCACACTCACTAAGCACACAGAGAATAATGTCTAGAATCTGAGTGCCATGTTATCAAATTGTACTGAGACTCTTGCAGTCACACAGGCTGACATGTAAGCATCGCCATGCCTAGTACAGACTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/v1.1.0-dev1/v1.1.0-dev1/ref2.fasta.fai b/v1.1.0-dev1/v1.1.0-dev1/ref2.fasta.fai new file mode 100644 index 000000000..e5d66331d --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/ref2.fasta.fai @@ -0,0 +1,5 @@ +0$chr1$9001$11468 2567 19 2567 2568 +1$chr1$53713$55817 2204 2607 2204 2205 +2$chr1$65161$67630 2569 4832 2569 2570 +3$chr1$82792$85041 2349 7422 2349 2350 +4$chr1$98000$100116 2216 9793 2216 2217 diff --git a/v1.1.0-dev1/v1.1.0-dev1/egrep-stderr-mediumcut.cwl b/v1.1.0-dev1/v1.1.0-dev1/stderr-mediumcut.cwl similarity index 65% rename from v1.1.0-dev1/v1.1.0-dev1/egrep-stderr-mediumcut.cwl rename to v1.1.0-dev1/v1.1.0-dev1/stderr-mediumcut.cwl index ef28494b0..7d4cf2b43 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/egrep-stderr-mediumcut.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/stderr-mediumcut.cwl @@ -2,17 +2,12 @@ class: CommandLineTool cwlVersion: v1.1.0-dev1 doc: "Test of capturing stderr output in a docker container." -hints: - DockerRequirement: - dockerPull: debian:wheezy - +requirements: + ShellCommandRequirement: {} inputs: [] - outputs: output_file: type: stderr - -baseCommand: egrep -successCodes: [2] - +arguments: + - { valueFrom: "echo foo 1>&2", shellQuote: False } stderr: std.err diff --git a/v1.1.0-dev1/v1.1.0-dev1/egrep-stderr-shortcut.cwl b/v1.1.0-dev1/v1.1.0-dev1/stderr-shortcut.cwl similarity index 63% rename from v1.1.0-dev1/v1.1.0-dev1/egrep-stderr-shortcut.cwl rename to v1.1.0-dev1/v1.1.0-dev1/stderr-shortcut.cwl index 0908dff35..4d6cc5fdd 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/egrep-stderr-shortcut.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/stderr-shortcut.cwl @@ -2,15 +2,11 @@ class: CommandLineTool cwlVersion: v1.1.0-dev1 doc: "Test of capturing stderr output in a docker container." -hints: - DockerRequirement: - dockerPull: debian:wheezy - +requirements: + ShellCommandRequirement: {} inputs: [] - outputs: output_file: type: stderr - -baseCommand: egrep -successCodes: [2] +arguments: + - { valueFrom: "echo foo 1>&2", shellQuote: False } diff --git a/v1.1.0-dev1/v1.1.0-dev1/egrep-stderr.cwl b/v1.1.0-dev1/v1.1.0-dev1/stderr.cwl similarity index 68% rename from v1.1.0-dev1/v1.1.0-dev1/egrep-stderr.cwl rename to v1.1.0-dev1/v1.1.0-dev1/stderr.cwl index b1bbcfd0b..74a6941c4 100644 --- a/v1.1.0-dev1/v1.1.0-dev1/egrep-stderr.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/stderr.cwl @@ -2,14 +2,13 @@ class: CommandLineTool cwlVersion: v1.1.0-dev1 doc: "Test of capturing stderr output in a docker container." -hints: - DockerRequirement: - dockerPull: debian:wheezy +requirements: + ShellCommandRequirement: {} inputs: [] outputs: output_file: type: File outputBinding: {glob: error.txt} -baseCommand: egrep -successCodes: [2] +arguments: + - { valueFrom: "echo foo 1>&2", shellQuote: False } stderr: error.txt diff --git a/v1.1.0-dev1/v1.1.0-dev1/test-cwl-out2.cwl b/v1.1.0-dev1/v1.1.0-dev1/test-cwl-out2.cwl new file mode 100644 index 000000000..d8c5f9ac5 --- /dev/null +++ b/v1.1.0-dev1/v1.1.0-dev1/test-cwl-out2.cwl @@ -0,0 +1,18 @@ +class: CommandLineTool +cwlVersion: v1.1.0-dev1 +requirements: + - class: ShellCommandRequirement +hints: + DockerRequirement: + dockerPull: "debian:wheezy" + +inputs: [] + +outputs: + - id: foo + type: File + +arguments: + - valueFrom: > + echo foo > foo && echo '{"foo": {"location": "file://$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json + shellQuote: false diff --git a/v1.1.0-dev1/v1.1.0-dev1/tmap-tool.cwl b/v1.1.0-dev1/v1.1.0-dev1/tmap-tool.cwl index 57228f3ea..d9ea0fb75 100755 --- a/v1.1.0-dev1/v1.1.0-dev1/tmap-tool.cwl +++ b/v1.1.0-dev1/v1.1.0-dev1/tmap-tool.cwl @@ -38,7 +38,8 @@ "glob": "output.sam" }, "type": ["null", "File"] - } + }, + {"id": "args", "type": "string[]"} ], "requirements": [ {"class": "SchemaDefRequirement",