Error at parse_runs step about distiller-nf HOT 4 CLOSED

That's because parameter drop_sam in the project.yml is commented, thus it evaluates to null by nextflow, and toBoolean(null) is an error now.

https://github.com/mirnylab/distiller-nf/blob/09a9b41567587384ccb39c76da49f7986f381789/project.yml#L60

All the required parameters are now uncommented in the project.yml by default, and should remain as such.

@golobor this can be closed

from distiller-nf.

closing it, but with some extra info:

params['map'].get('drop_sam','false')
uses this get() method: http://docs.groovy-lang.org/docs/groovy-1.7.3/html/groovy-jdk/java/util/Map.html#get(K, V)

the second value is the default value, which is returned when the requested key is missing. Thus, in my understanding, if drop_sam is commented out, it should return 'false', not null.

Also, I commented out drop_sam and did not get any error, which probably implies that the observed error was in old code and is fixed now.

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I remember the Travis builds were failing when some of the options were commented in project.yml, with the same error (toBoolean(null)), and uncommenting them were sufficient to fix them.
Some funky docker-related issue maybe?

This could be rediscovered with the next distiller commit, one could comment out drop_sam or something like that, and see if Travis would pass

from distiller-nf.

i wouldn't blame docker where it could be our issues :)
anyways, let's see if any similar issue pops up in the future

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