Re: Preparing for a new release

[zimoun <zimon.toutoune@gmail.com>]

On Mon, 10 Feb 2020 at 02:25, Kyle Meyer <kyle@kyleam.com> wrote:
>
> zimoun <zimon.toutoune@gmail.com> writes:
>
> > On Sun, 9 Feb 2020 at 14:01, Ricardo Wurmus <rekado@elephly.net> wrote:
> >
> >> * inputs and outputs are not validated
> >>
> >>   When a process declares that it produces an output, but then doesn’t do
> >>   that, the next process will fail with a nasty error message.  This is
> >>   especially nasty when using containerization as the error is about
> >>   failing to map the input into the container.
> >>
> >>   Processes should automatically validate their inputs and outputs.
> >>   Since inputs and outputs could technically be something other than
> >>   files I’m not sure exactly how to do this.
> >
> > From my understanding, Snakemake uses only files as inputs/outputs.
> > But I do not know what happens if 'rule 1' claims to output 'file' and
> > 'rule 2' says its input is 'file' and then 'rule 1' never produces
> > this file 'file'; the 'rule 2' is never processed, I guess. Hum? need
> > to check...
>
> In that case, an exception is raised:
>
>     Waiting at most 5 seconds for missing files.
>     MissingOutputException in line 2 of /tmp/snakemake-hAlqJ/Snakefile:
>     Missing files after 5 seconds:
>     foo
>     This might be due to filesystem latency. If that is the case, consider
>     to increase the wait time with --latency-wait.
>     Shutting down, this might take some time.

Thank you for checking.


All the best,
simon