From mboxrd@z Thu Jan 1 00:00:00 1970 MIME-Version: 1.0 References: <87h801p818.fsf@elephly.net> <87h800u84z.fsf@kyleam.com> <87a75spx3i.fsf@elephly.net> <877e0vq5iy.fsf@elephly.net> <87tv3z2pyf.fsf@kyleam.com> In-Reply-To: <87tv3z2pyf.fsf@kyleam.com> From: zimoun Date: Mon, 10 Feb 2020 08:34:03 +0100 Message-ID: Subject: Re: Preparing for a new release Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable To: Kyle Meyer Cc: Ricardo Wurmus , gwl-devel@gnu.org List-ID: On Mon, 10 Feb 2020 at 02:25, Kyle Meyer wrote: > > zimoun writes: > > > On Sun, 9 Feb 2020 at 14:01, Ricardo Wurmus wrote: > > > >> * inputs and outputs are not validated > >> > >> When a process declares that it produces an output, but then doesn= =E2=80=99t do > >> that, the next process will fail with a nasty error message. This i= s > >> 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=E2=80=99m 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, conside= r > to increase the wait time with --latency-wait. > Shutting down, this might take some time. Thank you for checking. All the best, simon