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

Question

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?

Eric C. · Accepted Answer · 2019-01-08T15:08:19.043

3

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

edited Jan 08 '19 at 15:08

answered Nov 21 '17 at 16:39

Eric C.

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Maybe @vodka knows an answer? – mox Feb 05 '19 at 12:42

score 3 · Answer 2 · edited Feb 05 '19 at 14:58

3

snakemake -p -n

Avoid the --quiet reported in the @eric-c answer, at least in some situations the combination on -p -n -q does not print the command executed without -n.

edited Feb 05 '19 at 14:58

Kamil S Jaron

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answered Feb 05 '19 at 12:51

mox

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In my snakemake 5.2.2, this also prints rules, input, output etc... which, from what I understood of the question, was not what was asked. I cannot find a way to print only the shell commands ! – Eric C. Feb 06 '19 at 10:39

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

2 Answers2