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I want to export the DAG of my workflow in D3.js compatible JSON format: 

snakemake.snakemake(snakefile=smfile,
                    dryrun=True,
                    forceall=True,
                    printdag=False,
                    printd3dag=True,
                    keepgoing=True,
                    cluster_config=cluster_config,
                    configfile=configfile,
                    targets=targetfiles)

Unfortunately, it complains about missing input files.

It is right about the fact that the files are missing but I had hoped that it would run anyways, especially after setting the keepgoing option to True.

Is there a smart way to export the DAG without the input files?

Thanks, Jan

Jan Schreiber
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1 Answers1

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--keep-going allows execution of independent jobs if a snakemake job fails. That is, snakemake has to successfully start running jobs. In your case, it never gets to that stage. I would imagine missing input files would not allow creation of DAG.

Manavalan Gajapathy
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  • Thanks for your answer. I chose a workaround that parses the error messages from snakemake and creates dummy input files. This runs in a loop until no `MissingInputException` occurs any more. – Jan Schreiber Aug 28 '18 at 08:22