Issue #70 resolved

phony rules (with no output) should always be run

Jeremy Leipzig
created an issue

I have a rule that performs an operation but has no file output

rule publishdata:
    input: BIGWIGS, QCED, "diffExp.pdf", GAGE_GO_FILES
        rsync -v --update --rsh=ssh -r diffExp.pdf muscleResults.csv heartResults.csv fastqc tracks RNASEQC_DIR {GAGE_GO_FILES} {MITOMAP}

This rule doesn't run until I --force it. In my thinking it should always run.

snakemake -npr publishdata
Nothing to be done.
(snake-env)[leipzig@raboso snake-env]$ snakemake publishdata
(snake-env)[leipzig@raboso snake-env]$ snakemake --force publishdata
Provided cores: 1
Job counts:
    count   jobs
    1   publishdata

Comments (3)

  1. Johannes Köster repo owner

    Hi, so far the behaviour is that publishdata would be executed iff one of the input files was updated in the same run. But you are right, if there is a shell or run declatation, it should be always executed if selected as a target. I changed the behaviour in the current git master.

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