Create snakemake.txt

docs/chatbot_comparison/knowledge_testing/snakemake.txt

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+1. Question: How do you define a rule in Snakemake, and what are the essential components of a rule?
+
+Expected Answer: A rule in Snakemake is defined using the rule keyword followed by a rule name. Essential components include input, output, and shell or script. For example:
+Python
+```
+rule example:
+    input: "input_file.txt"
+    output: "output_file.txt"
+    shell: "cat {input} > {output}"
+```
+
+2. Question: How does Snakemake handle dependencies between rules, and how can you specify that one rule depends on the output of another?
+
+Expected Answer: Snakemake handles dependencies by specifying the output of one rule as the input of another. This creates a directed acyclic graph (DAG) of jobs. For example:
+Python
+```
+rule first_rule:
+    output: "intermediate_file.txt"
+    shell: "echo 'data' > {output}"
+
+rule second_rule:
+    input: "intermediate_file.txt"
+    output: "final_output.txt"
+    shell: "cat {input} > {output}"
+```
+
+3. Question: What are wildcards in Snakemake, and how are they used in rule definitions?
+Expected Answer: Wildcards in Snakemake are placeholders that match parts of filenames and allow for flexible rule definitions. They are enclosed in curly braces {}. For example:
+Python
+```
+rule all:
+    input: expand("results/{sample}.txt", sample=["sample1", "sample2"])
+
+rule process:
+    input: "data/{sample}.txt"
+    output: "results/{sample}.txt"
+    shell: "cp {input} {output}"
+```