having no map options, i.e. empty dict, leads to nextflow error

[sergpolly]

we commented the extra mapping options in the project.yml:
https://github.com/mirnylab/distiller-nf/blob/5b5da693f3835e2ed57635fbda13ef0d170c4f29/test/test_project.yml#L99

and the whole thing crashed - nextflow/groovy level crash that was:

N E X T F L O W  ~  version 19.01.0
Launching `distiller.nf` [berserk_kowalevski] - revision: c454203cd8
ERROR ~ Cannot invoke method get() on null object

 -- Check script 'distiller.nf' at line: 110 or see '.nextflow.log' file for more details

we should check into how are we using map dictionary and prevent crashes like that ...

[golobor]

yes, this and other issues are caused by the fact that we do not validate project.yaml's. Since there are so many different parameters to check, we would need some kind of generic approach. There is an ongoing discussion on how to implement such a feature in core nextflow: nextflow-io/nextflow#866 , but it seems to have stuck. Should we just implement something of our own?

…

On Tue, 14 May 2019 at 18:10, Sergey Venev ***@***.***> wrote: we commented the extra mapping options in the project.yml: https://github.com/mirnylab/distiller-nf/blob/5b5da693f3835e2ed57635fbda13ef0d170c4f29/test/test_project.yml#L99 and the whole thing crashed - nextflow/groovy level crash that was: N E X T F L O W ~ version 19.01.0 Launching `distiller.nf` [berserk_kowalevski] - revision: c454203cd8 ERROR ~ Cannot invoke method get() on null object -- Check script 'distiller.nf' at line: 110 or see '.nextflow.log' file for more details we should check into how are we using map dictionary and prevent crashes like that ... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#142>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAG64CQBOUGFXPXYJKLZIKTPVM2GBANCNFSM4HM6CCEA> .