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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:
    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.

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