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 #91 & #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 _genemodel in the workflow_input.yml file, is correct in Episode 3
Remove RAM requirements from _mappingreads step
Add output from the _quality_controlforward and _quality_controlreverse steps to outputs -> maybe an exercise?
Add command to run the multi-step workflow
Episode 3 - Resources for Reusing Tools and Scripts:
Add the _indexallignment step, this is never mentioned, except in the exercise. Some people miss this step and get error when running the _countreads step without the _indexallignment 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.
These are the notes I took during the pilot workshop at the VU on Thursday March 24th.
General notes:
Episode 1 - CWL and Shell Tools:
Episode 2 - Developing Multi-Step Workflows:
Episode 3 - Resources for Reusing Tools and Scripts:
step_name/output, is missing in the text.Episode 4 - Debugging Workflows:
--debugcommand