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Use this tag to refer to the questions related to snakemake

2
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The Snakemake documentation just links to the Python re module documentation. … Edit: I think I found the issue in the snakemake source. …
answered Dec 3 '20 by Jesse
1
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Here's a clumsy little example using a fake job submission script: https://github.com/ressy/example-snakemake-profiles The current documentation makes it sound like cluster configuration support is … introduction of Profiles. ...but from those example profiles, that might be misleading; here's an example template for a profile YAML that references a separate cluster-config YAML: https://github.com/Snakemake-Profiles …
answered Feb 19 '20 by Jesse
1
vote
I don't think Snakemake can follow a "use any of these" pattern with a unified dependency graph and without additional assumptions, but you can do it if you break the workflow into two pieces. … shell: "echo {input} &&" "touch {output}" rule create_somefile: output: "somefile_{n_dims}.json" shell: "touch {output}" For example if you have somefile_2.json already there: $ snakemake
answered Oct 10 '21 by Jesse
2
votes
Current working directory: /home/jesse/dev/snakemake-wd/working-directory Building DAG of jobs... Nothing to be done. … Complete log: /home/jesse/dev/snakemake-wd/working-directory/.snakemake/log/2019-08-02T142009.349338.snakemake.log …
answered Aug 2 '19 by Jesse
1
vote
Each expand() makes a list, so at first Snakemake sees two lists back-to-back and doesn't know what to do with them. … You can even comment out all the Snakemake-specific syntax and leave just Python code when debugging, to sanity-check the rest of the code (e.g. your inputs and outputs from expand). …
answered Nov 12 '21 by Jesse