### Loop Example

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/loop.md

An example demonstrating the cwltool:Loop requirement with a loop condition and output method.

```yaml
example:
  run:
    class: ExpressionTool
    inputs:
      i1: int
    outputs:
      o1: int
    expression: >
      ${return {'o1': inputs.i1 + 1};}
  in:
    i1: i1
  out: [o1]
  requirements:
    cwltool:Loop:
      loopWhen: $(inputs.i1 < 10)
      loop:
        i1: o1
      outputMethod: last

```

--------------------------------

### Running a partial workflow with a target step

Source: https://github.com/common-workflow-language/cwltool/blob/main/README.rst

Example command to run a workflow starting from a specific step.

```bash
cwltool --target step3 my-wf.cwl
```

--------------------------------

### Install the latest development version of cwltool

Source: https://github.com/common-workflow-language/cwltool/blob/main/README.rst

This snippet shows how to clone the cwltool repository, navigate into the directory, install it from source with dependencies, and verify the installation.

```bash
git clone https://github.com/common-workflow-language/cwltool.git # clone (copy) the cwltool git repository
cd cwltool           # Change to source directory that git clone just downloaded
pip install .[deps]  # Installs ``cwltool`` from source
cwlt ool --version    # Check if the installation works correctly
```

--------------------------------

### Option two specific example using SoftwareRequirement packages

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/concepts.md

A specific example using the compact map syntax for SoftwareRequirement packages.

```yaml
hints:
  SoftwareRequirement:
    packages:
      sourmash:
        specs: [ https://doi.org/10.21105/joss.00027 ]
      screed:
        version: [ "1.0" ]
      python: {}
```

--------------------------------

### Install cwltool development version

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/index.md

Clones the cwltool repository and installs the latest development version from source.

```bash
git clone https://github.com/common-workflow-language/cwltool.git
cd cwltool
pip install .[deps]
cwltool --version
```

--------------------------------

### Option two specific example using Workflow inputs

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/concepts.md

A specific example using the compact map syntax for Workflow inputs.

```yaml
inputs:
  workflow_input01:
    type: string
  workflow_input02:
    type: File
    format: http://edamontology.org/format_2572
```

--------------------------------

### Option two generic example

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/concepts.md

A generic example of the compact map syntax where a key field becomes the map key.

```yaml
some_cwl_field:
  a_complex_type1:  # this was the "key_field" from above
    field2: foo
    field3: bar
  a_complex_type2:
    field2: foo2
    field3: bar2
  a_complex_type3: {}  # we accept the defualt values for "field2" and "field3"
```

--------------------------------

### Workflow Execution Provenance

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/CWLProv.md

Example of PROV-JSON representation for starting a workflow run.

```default
activity(id:67f38794-d24a-435f-bd4a-0242a56a581b, 2018-04-16T18:27:09.428165, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"])
wasStartedBy(id:67f38794-d24a-435f-bd4a-0242a56a581b, -, id:7c9d9e88-666b-4977-85f4-c02da08a942d, 2018-04-16T18:27:09.428285)
```

--------------------------------

### Include Example: include.txt

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md

A text file to be included.

```text
hello world


```

--------------------------------

### Running basic tests

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/index.md

Command to run basic tests after installing cwltool.

```bash
pip install -rtest-requirements.txt
pytest   ## N.B. This requires node.js or docker to be available
```

--------------------------------

### Install cwltool using pip (when installing alongside other CWL implementations)

Source: https://github.com/common-workflow-language/cwltool/blob/main/README.rst

This command installs only the cwltool package using pip, recommended when installing alongside other CWL implementations.

```bash
pip install cwltool
```

--------------------------------

### Basic SoftwareRequirement Example

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/index.md

Command to run cwltool with a basic dependency resolver configuration.

```bash
cwltool --beta-dependency-resolvers-configuration tests/test_deps_env_resolvers_conf.yml \
    tests/random_lines.cwl \
    tests/random_lines_job.json
```

--------------------------------

### Running Tests with Tox

Source: https://github.com/common-workflow-language/cwltool/blob/main/CONTRIBUTING.md

Example of running specific tests (unit and type tests for Python 3.7) using tox.

```bash
tox -e py37-mypy
```

--------------------------------

### Installing Dependencies and Development Tools

Source: https://github.com/common-workflow-language/cwltool/blob/main/CONTRIBUTING.md

Command to install CWLTool in development mode with necessary tools.

```bash
make install-dep dev
```

--------------------------------

### Creating and Activating a Virtual Environment

Source: https://github.com/common-workflow-language/cwltool/blob/main/CONTRIBUTING.md

Steps to create a Python virtual environment for development.

```bash
python3 -m venv cwltool
source venv/bin/activate
```

--------------------------------

### Install CWL test parser

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/index.md

Installs the CWL test parser using pip.

```bash
pip install cwltest
```

--------------------------------

### Loop-independent iterations with 'all' output method

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/loop.md

An example demonstrating loop-independent iterations where each iteration can be processed concurrently.

```yaml
example:
  run: inner.cwl
  in:
    i1: i1
  out: [o1]
  requirements:
    cwltool:Loop:
      loopWhen: $(inputs.i1 < 10)
      loop:
        i1:
          valueFrom: $(inputs.i1 + 1)
      outputMethod: all
```

--------------------------------

### Install CWL reference runner

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/index.md

Installs the CWL reference runner using pip.

```bash
pip install cwlref-runner
```

--------------------------------

### Option three generic example

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/concepts.md

A generic example of a more compact option where only key fields are specified.

```yaml
some_cwl_field:
  a_complex_type1: foo   # we accept the default value for field3
  a_complex_type2: foo2  # we accept the default value for field3
  a_complex_type3: {}    # we accept the default values for "field2" and "field3"
```

--------------------------------

### Option one generic example

Source: https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/v1.2/concepts.md

A generic example of the verbose array format for map-like structures.

```yaml
some_cwl_field:
  - key_field: a_complex_type1
    field2: foo
    field3: bar
  - key_field: a_complex_type2
    field2: foo2
    field3: bar2
  - key_field: a_complex_type3
```

--------------------------------

### Printing Workflow Targets

Source: https://github.com/common-workflow-language/cwltool/blob/main/docs/index.md

Examples of using --print-targets and --print-subgraph to inspect workflow targets.

```bash
cwltool --print-targets my-wf.cwl
```

```bash
cwltool --target step3 --print-subgraph my-wf.cwl > my-wf-starting-from-step3.cwl
```