list

list

list or ls can be used to list all existing CWL Workflows and Tools. Using the command without the -a flag just ouputs the names of all existing CWL files in the project. Using the -all (or -a) flag will also output the tools in- and outputs which than can easily be used for the connect command.

Usage

Lists either all CWL Files or details to a given file

Usage: s4n list [OPTIONS] [FILE]

Arguments:
  [FILE]

Options:
  -a, --all   Outputs the tools with inputs and outputs
  -h, --help  Print help

Example

Simple Usage:

> s4n list
📂 Available CWL Files in: /mnt/m4.4_sciwin_client
📄 test-wf_features (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data
📄 echo_id (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 default (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 remote (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 mkdir_wf (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data
📄 read_bin (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 wf_inout (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data
📄 plot (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data/hello_world/workflows/plot
📄 main (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data/hello_world/workflows/main
📄 calculation (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data/hello_world/workflows/calculation
📄 test_expr (ExpressionTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 mkdir (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 wf_inout_dir (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data
📄 array_test (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 echo (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data
📄 test-wf (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data
📄 calculation_packed (CommandLineTool) in /mnt/m4.4_sciwin_client/tests/test_data/packed
📄 wf_inout_file (Workflow) in /mnt/m4.4_sciwin_client/tests/test_data
📄 plot (CommandLineTool) in /mnt/m4.4_sciwin_client/crates/remote-execution/tests/test_data/hello_world/workflows/plot
📄 main (Workflow) in /mnt/m4.4_sciwin_client/crates/remote-execution/tests/test_data/hello_world/workflows/main
📄 calculation (CommandLineTool) in /mnt/m4.4_sciwin_client/crates/remote-execution/tests/test_data/hello_world/workflows/calculation

Outputting details with -a:

> s4n list -a
📂 Available CWL Files in: /mnt/m4.4_sciwin_client
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| Tool                                 | Inputs                                                                 | Outputs                          |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| test-wf_features (Workflow)          | test-wf_features/pop                                                   | test-wf_features/out             |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| echo_id (CommandLineTool)            | echo_id/test                                                           | echo_id/results                  |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| default (CommandLineTool)            | default/file1                                                          | default/out                      |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| remote (CommandLineTool)             | remote/file                                                            |                                  |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| mkdir_wf (Workflow)                  | mkdir_wf/dirname                                                       | mkdir_wf/out                     |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| read_bin (CommandLineTool)           | read_bin/data                                                          | read_bin/output                  |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| wf_inout (Workflow)                  | wf_inout/first                                                         | wf_inout/last                    |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| plot (CommandLineTool)               | plot/results                                                           | plot/o_results                   |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| main (Workflow)                      | main/population, main/speakers                                         | main/out                         |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| calculation (CommandLineTool)        | calculation/population, calculation/speakers                           | calculation/results              |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| test_expr (ExpressionTool)           | test_expr/message                                                      | test_expr/uppercase_message      |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| mkdir (CommandLineTool)              | mkdir/dirname                                                          | mkdir/out                        |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| wf_inout_dir (Workflow)              | wf_inout_dir/dir                                                       | wf_inout_dir/newdir              |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| array_test (CommandLineTool)         |                                                                        | array_test/array                 |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| echo (CommandLineTool)               | echo/test                                                              | echo/results                     |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| test-wf (Workflow)                   | test-wf/pop                                                            | test-wf/out                      |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| calculation_packed (CommandLineTool) | calculation_packed/#main/population, calculation_packed/#main/speakers | calculation_packed/#main/results |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| wf_inout_file (Workflow)             | wf_inout_file/file                                                     | wf_inout_file/newfile            |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| plot (CommandLineTool)               | plot/results                                                           | plot/results                     |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| main (Workflow)                      | main/population, main/speakers                                         | main/out                         |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+
| calculation (CommandLineTool)        | calculation/population, calculation/speakers                           | calculation/results              |
+--------------------------------------+------------------------------------------------------------------------+----------------------------------+

Listing a specific file:

> s4n list tests/test_data/hello_world/workflows/main/main.cwl
🔎 Workflow: `tests/test_data/hello_world/workflows/main/main.cwl`
_________________________________________________________________
CWL Version:    v1.2
_________________________________________________________________
Connection status:
+--------------------------------+------------------+-----------------+
| Tool                           | Inputs           | Outputs         |
+================================+==================+=================+
| <Workflow>                     | ✅    population | ✅    out       |
|                                | ✅    speakers   |                 |
+--------------------------------+------------------+-----------------+
| Steps:                         |                  |                 |
+--------------------------------+------------------+-----------------+
| ../calculation/calculation.cwl | ✅    population | ✅    results   |
|                                | ✅    speakers   |                 |
+--------------------------------+------------------+-----------------+
| ../plot/plot.cwl               | ✅    results    | ✅    o_results |
+--------------------------------+------------------+-----------------+
✅ : connected - 🔘 : tool default - ❌ : no connection