These are chat archives for nextflow-io/nextflow

18th
Sep 2015
Matthieu Foll
@mfoll
Sep 18 2015 14:31
Hi Paolo
Paolo Di Tommaso
@pditommaso
Sep 18 2015 14:31
hi
Matthieu Foll
@mfoll
Sep 18 2015 14:32
So NXF_VERgives me nextflowversion (that I can use to write in my output for records)
Paolo Di Tommaso
@pditommaso
Sep 18 2015 14:32
yep
Matthieu Foll
@mfoll
Sep 18 2015 14:33
I would like to have also a variable for the pipeline version from github (if defined)
Paolo Di Tommaso
@pditommaso
Sep 18 2015 14:33
actually there's the script commit ID in log file
you want to save to a different file ?
Matthieu Foll
@mfoll
Sep 18 2015 14:34
yes
in the output of my pipeline
Paolo Di Tommaso
@pditommaso
Sep 18 2015 14:34
I see
Matthieu Foll
@mfoll
Sep 18 2015 14:35
in order that when user have (and share) their results all the version numbers are written inside
for reproducibility
Paolo Di Tommaso
@pditommaso
Sep 18 2015 14:35
if so I think it would be better to use an implicit java.groovy object holding some runtime info
does it sounds fine to you ?
Matthieu Foll
@mfoll
Sep 18 2015 14:58
sorry I get interupted
I’m not sure I see in practice what would be the difference, but as long as I can access the info during runtime that’s fine
Paolo Di Tommaso
@pditommaso
Sep 18 2015 14:59
no pb
ok
Matthieu Foll
@mfoll
Sep 18 2015 14:59
and having also the docker Image ID would be cool
and why not the full command line
Paolo Di Tommaso
@pditommaso
Sep 18 2015 15:00
what do you mean by full command line?
Matthieu Foll
@mfoll
Sep 18 2015 15:00
yes
Paolo Di Tommaso
@pditommaso
Sep 18 2015 15:01
the same as the command line that is output in the log file ?
Matthieu Foll
@mfoll
Sep 18 2015 15:01
exactly
Paolo Di Tommaso
@pditommaso
Sep 18 2015 15:01
ok
a bit more complex for the docker image
since a pipeline could use a different one for each process
Matthieu Foll
@mfoll
Sep 18 2015 15:02
ah yes I don’t use that so I forgot about this option
Paolo Di Tommaso
@pditommaso
Sep 18 2015 15:02
however the used containers are included in the trace file
Matthieu Foll
@mfoll
Sep 18 2015 15:03
indeed
I think a good practice anyway is to ask users to also keep/publish the .nextflow.log and trace files
I’ll add that in my pipeline documentation
Paolo Di Tommaso
@pditommaso
Sep 18 2015 15:04
it makes sense