Snakemake MissingRuleException

Question

I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message.

Error: Building DAG of jobs...
MissingRuleException:
No rule to produce snakefile (if you use input functions make sure that they don't raise unexpected exceptions).

Code:

rule salmon_index:
        input:
                R1="sequences/*R1.fastq.gz",
                R2="sequences/*R2.fastq.gz"
        output:
                Index="results/salmon_index"
        shell:
                """
                salmon index --threads 8 -t references/genome.fa.gz -i salmon_index
                """

Answer 1

You're not using wildcards the way snakemake is equipped to work with them. See:

1. FAQs such as https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory and https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do
2. https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards