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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
66 stars 44 forks source link

config.yaml is not part of the release download #56

Closed cmeesters closed 2 years ago

cmeesters commented 2 years ago

Hi,

very nice workflow! I would, however, suggest including the config-directory as a sample directory in the release, otherwise users have to download everything separately (or clone the development branch).

Best regards Christian

johanneskoester commented 2 years ago

Thanks! As the readme says, the usage is described in the workflow catalog, see here: https://snakemake.github.io/snakemake-workflow-catalog?usage=snakemake-workflows/rna-seq-kallisto-sleuth

When following the steps over there, you get a correct deployment of the workflow including the template config. It is no longer best practice to simply clone snakemake workflows. Instead one uses them as modules like shown in the catalog link above. The advantage is that it becomes very easy to follow the upstream versions and also to compose multiple workflows together.