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snakemake

Is it possible to print commands instead of rules in snakemake dry run?

Dry runs are a super important functionality of workflow languages. What I am looking at is mostly what would be executed if I run the command and this is exactly what one see when running make -n.

However analogical functionality snakemake -n prints something like

Building DAG of jobs...

rule produce_output:
    output: my_output
    jobid: 0
    wildcards: var=something

Job counts:
    count   jobs
    1   produce_output
    1

The log contains kind of everything else than commands that get executed. Is there a way how to get command from snakemake?

Solution 
  • snakemake -p --quiet -n

    -p for print shell commands
    -n for dry run
    --quiet for removing the rest

    EDIT 2019-Jan

    This solution seems broken for lasts versions of snakemake