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Re: Preparing for a new release
From: |
Kyle Meyer |
Subject: |
Re: Preparing for a new release |
Date: |
Mon, 10 Feb 2020 01:25:44 +0000 |
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.
- 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