What changes invalidate snakemake pipeline

Asked Dec 14 '20 at 13:59

Active Dec 14 '20 at 13:59

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It is not clear what changes will invalidate the pipeline and prompt snakemake to re-run the workflow.

Does change in input, intermediate output or custom script re-run the pipeline? In my experience changing intermediate output and custom script does not invalidate the pipeline and having that feature may improve reproducibility.

asked Dec 14 '20 at 13:59

leo

2

[Q&A](https://stackoverflow.com/q/62419042/3998252) here would partly answer this question. – Manavalan Gajapathy Dec 14 '20 at 14:12
Thanks! @ManavalanGajapathy have you filed an issue? – leo Dec 14 '20 at 14:29
1

@timing, it is clearly defined behavior.. You can update the timestamps of all your outputs with `--forceall --touch`. – Maarten-vd-Sande Dec 14 '20 at 16:15
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@timing [Yes](https://github.com/snakemake/snakemake/issues/449) – Manavalan Gajapathy Dec 14 '20 at 16:38
@Maarten-vd-Sande thanks! some tools like targets-r-package support monitoring of scripts and inputs so i was expecting that from snakemake too... – leo Dec 14 '20 at 18:02

What changes invalidate snakemake pipeline

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