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Re: Preparing for a new release
From: |
zimoun |
Subject: |
Re: Preparing for a new release |
Date: |
Mon, 10 Feb 2020 08:34:03 +0100 |
On Mon, 10 Feb 2020 at 02:25, Kyle Meyer <address@hidden> wrote:
>
> zimoun <address@hidden> writes:
>
> > On Sun, 9 Feb 2020 at 14:01, Ricardo Wurmus <address@hidden> 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
- Preparing for a new release, Ricardo Wurmus, 2020/02/08
- Re: Preparing for a new release, Kyle Meyer, 2020/02/08
- Re: Preparing for a new release, Ricardo Wurmus, 2020/02/08
- Re: Preparing for a new release, Ricardo Wurmus, 2020/02/10
- Re: Preparing for a new release, zimoun, 2020/02/10
- Re: Preparing for a new release, Ricardo Wurmus, 2020/02/10
- Re: Preparing for a new release, zimoun, 2020/02/10
- Re: Preparing for a new release, Ricardo Wurmus, 2020/02/11
- Re: Preparing for a new release, Ricardo Wurmus, 2020/02/11
- Re: Preparing for a new release, zimoun, 2020/02/11