Description
In the Snakemake Profile section, the cluster_profile/config.yaml file is introduced with options to copy-paste, but two issues reduce clarity:
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No explanation of the options: the config.yaml contents are presented without describing what each option does or why it is set the way it is. Only by pattern matching one can guess that the options of the snakemake command are used as args in the config.yaml.
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Inconsistent values: the config file uses jobs: 3, but all preceding examples in the lesson used -j1 (--jobs 1). This inconsistency is not acknowledged or explained, which may confuse learners who notice the discrepancy.
Suggested improvements
Description
In the Snakemake Profile section, the
cluster_profile/config.yamlfile is introduced with options to copy-paste, but two issues reduce clarity:No explanation of the options: the
config.yamlcontents are presented without describing what each option does or why it is set the way it is. Only by pattern matching one can guess that the options of the snakemake command are used as args in the config.yaml.Inconsistent values: the config file uses
jobs: 3, but all preceding examples in the lesson used-j1(--jobs 1). This inconsistency is not acknowledged or explained, which may confuse learners who notice the discrepancy.Suggested improvements
config.yaml, similar to how options were introduced at the command line.jobsvalue with what was used previously (jobs: 1), or explicitly explain why a different value is used in the profile.