common workflow language parser

Question

[sahiilseth]

Is there a way to create a list of all commands which need to run as part of the pipeline?

For example:

cwl-parser  hello.cwl

would create a table like this:

|jobname    |cmd                                                            |
|:----------|:--------------------------------------------------------------|
|sleep      |sleep 10 && sleep 2;echo hello                                 |
|sleep      |sleep 11 && sleep 8;echo hello                                 |
|sleep      |sleep 11 && sleep 17;echo hello                                |
|create_tmp |head -c 100000 /dev/urandom > sample1_tmp_1                    |
|create_tmp |head -c 100000 /dev/urandom > sample1_tmp_2                    |
|create_tmp |head -c 100000 /dev/urandom > sample1_tmp_3                    |
|merge      |cat sample1_tmp_1 sample1_tmp_2 sample1_tmp_3 > sample1_merged |
|size       |du -sh sample1_merged; echo MY shell: $SHELL                   |

Answer 1

[Michael R. Crusoe]

Yep, see https://github.com/common-workflow-language/cwl2script for an example. Let me know if it needs updating.