common workflow language parser
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 |
• 1,981 views
•
link
1 answer
Yep, see https://github.com/common-workflow-language/cwl2script for an example. Let me know if it needs updating.
• 1 views
•
link
Log in to answer this question.