2. Gene-regulation library¶
The library contains a variety of files, including scripts and configuration files.
You can find a description of these hereafter.
2.1. Snakemake files (snakefiles)¶
Snakefiles are based on the scripting language Python 3, and use a specific syntax.
For organization purpose, we have distinguished two types of Snakefiles:
- Rules are typically “bricks” to build workflows with. Each rule corresponds to a specific operation.
- Workflows are combinations of rules that serve a specific purpose: quality check of sequencing data, ChIP-seq peaks analysis...
2.1.2. Rules (.rules)¶
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2.2. Python scripts (.py)¶
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2.3. R scripts¶
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2.4. Configuration files (yaml)¶
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2.5. R markdown files (.Rmd)¶
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2.6. Tabulated files (.tab)¶
We use tabulated files in order to define and describe the samples to be processed in the workflows.
Examples of these files are available in the examples folder of the library.
2.6.1. Sample description files (samples.tab)¶
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2.6.2. Experimental design files (design.tab)¶
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