README.md

Workshop Github template and code recommendations

Provide the github link to participants for easy access to the data and sharing the material.

Structure and content

The github must have something similar to the following structure:

├── README.md # workshop overview, requirements and software, links to colab if used/etc. See README_template
├── Exercises
│   ├── data
│   │   └── datafile1
│   │   └── ...
│   ├── scripts
│   │   └── Exercise1.md and .html
│   │   └── script1.sh/py/r
│   └── answers/results
│       └── ...
├── Slides
│   └── workshopslides.pdf #using the pptx template provided
└── Outline
    └── workshopoutline.pdf #using the template provided

It is required to provide at least:

• Slides
• Scripts
• Data

Every workshop will have its own best way of providing scripts and data. Be mindful and organized so participants can easily access everything as the workshop proceeds (scripts, data and results must me reachable). Do not assume they will know where to find the data or where to store the results!!

Recommendations

Each workshop will have its own needs, so these are only broad recommendations. Consider the organization of the code and legibility as a must. If possible avoid expaining on top a sh/py/r scripts without annotations/clear documentation and use notebooks with separated blocks.

Data

• Be mindful about the dataset size and computational times in normal computers as not everyone will have the same computational power. Provide the smallest possible dataset to have results: subsets of the genome, small tables/txts files, etc.

For command-line UNIX-based workshops

• Provide the code in a markdown format (and html or pdf) so that participants can copy and paste the commands directly to the terminal
• If handson exercises are free code, provide a md document (and html or pdf) with the question, code answer(s) and output
• For more advanced workshops and if required (i.e as part of a pipeline), .sh scripts can be provided

For python-based workshops

• Use of google-colab notebooks is suggested, adding annotations for each part of the code.
• If handson exercises are free-code or fill in the blank, provide a different set of notebooks with the answers
• For more advanced workshops and if required, .py scripts can be provided

For R-based workshops

• Use of R-markdown notebooks in Rstudio is suggested, adding annotations for each part of the code.
• If handson are free-code or fill in the blank, provide a different set of notebooks with the answers
• For more advanced workshops and if required (i.e as part of a pipeline), .r scripts can be provided

Multi-tool workshops

Some workshops will require the usage of the command-line and R or python for further processing as part of a pipeline (i.e PRS and omics workshops). If possible, run shell commands inside the python/R notebooks; if not, provide a clear pipeline structure, i.e. as a notebook, so participants can follow each step.

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