Improvements and bugs during pilot workshop

[ALuesink]

These are the notes I took during the pilot workshop at the VU on Thursday March 24th.

General notes:

• All the episodes have no time set in the Overview box for Teaching and Exercises.
• Mention using the terminal in VS Code and then starting the virtual environment
• Check if all formats are https instead of http, also in bio-cwl-tools library (PR Fixed URLs for episode 2 #91 & Fix URLs file format requirement episode 4 #92)
• Is it necessary to download all 4 fastq files? In the tutorial only GSM461177_1_subsampled and GSM461177_2_subsampled are used.

Episode 1 - CWL and Shell Tools:

• The location of the rna_seq file is incorrect -> use an exercise to fix this

Episode 2 - Developing Multi-Step Workflows:

• Format field is missing for gene_model in the workflow_input.yml file, is correct in Episode 3
• Remove RAM requirements from mapping_reads step
• Add output from the quality_control_forward and quality_control_reverse steps to outputs -> maybe an exercise?
• Add command to run the multi-step workflow

Episode 3 - Resources for Reusing Tools and Scripts:

• Add the index_allignment step, this is never mentioned, except in the exercise. Some people miss this step and get error when running the count_reads step without the index_allignment step.
• The featureCounts tool is hard to find, it is actually in the subread folder in the bio-cwl-tools library
• In the first exercise, change CWL document to CWL file. Some people didn't understand that the CWL document of a tool is the CWL file of that tool.
• Remove the RAM exercise -> change to add the featureCounts tool
• Explain how to reference an output from a different step: step_name/output, is missing in the text.

Episode 4 - Debugging Workflows:

• The YML file is missing in the --debug command