Notes from CWL workshop 15 June

[RenskeW]

Here are the notes & proposed enhancements gathered at yesterday's workshop:

• [x] Fix the variable types in bio-cwl-tools/fastqc/fastqc_2.cwl (e.g. line 39 —> int?)
• [x] Provide students with list of all containers so they can pull them before the workshop
• [x] Rename workflow_input.yml and rna_seq_workflow.cwl to different filenames between the lessons (so students don’t need to edit their files in place but can just make a new file)
• [ ] Lesson “Resources…” --> specify which exact workflow should be run
• [x] Provide command-line option with - - cachedir to show people how to save intermediate outputs
• [x] Missing step in the workflow in section “Adding new step to workflow” —> makes example too complicated.
• [ ] Fix samtools_index to require a format for the bam-sorted input which would force us to change STAR align output to require formats to the inputs
• [x] Add format to gene_model, otherwise workflow execution fails (both in workflow input parameters and input parameter file)
• [ ] Figure out why Benten is erroneously complaining about ‘mapped_reads’ and ‘annotations’ variables
• [x] Lesson ‘Debugging workflows’: rename the workflow files (e.g. rna_bad_workflow.cwl)
• [ ] Last lesson ‘Resources’: add link to support resources where people can ask questions if they are stuck
• [ ] Comment at the end: longer live-coding session would be helpful
• [ ] Comment at the end: somebody had trouble installing cwltool on a Mac M1. Solution, needs documenting on the website

[gcapes]

Missing step in the workflow in section “Adding new step to workflow” —> makes example too complicated.

Duplicate of #105