These are chat archives for nextflow-io/nextflow

19th
Jun 2017
Paolo Di Tommaso
@pditommaso
Jun 19 2017 12:30
Join the discussion: Snakemake vs Nextflow
LukeGoodsell
@LukeGoodsell
Jun 19 2017 15:09

Hi, I’m having a problem with a Nextflow process that generates a yaml output file and a val output. I’ve put a demo nf script and the relevant section of the log in this gist: https://gist.github.com/LukeGoodsell/8b2ecb42658fd8be3b3ad77e13866a9a
Essentially, when a process has an output val, Snakeyaml complains that:

WARN: Cannot serialize context map. Cause: java.lang.IllegalArgumentException: type cannot be null. -- Resume will not work on this process

Any help you can provide would be greatly appreciated.

With the linked test.nf, when you comment-out the val output line, the process works, but without the required output.
Paolo Di Tommaso
@pditommaso
Jun 19 2017 15:31
define all variables that are not outputs local with def
def paramsObj = [:]
paramsObj['name'] = x.firstName + " " + x.lastName
def paramsFilePath = new File("${task.workDir}/params.yaml")
def yaml = new Yaml()
yaml.dump(paramsObj, new FileWriter(paramsFilePath))
LukeGoodsell
@LukeGoodsell
Jun 19 2017 15:40
Ahhh!
+1
Many thanks, Paolo
Matthieu Pichaud
@MatPich_twitter
Jun 19 2017 19:16
Hi there,
Thanks for the beautiful program.
Is it possible to have the folder PublishDir inspected, and not only workDir, to check if a process is complete / needs to be run with -resume?
Matthieu Pichaud
@MatPich_twitter
Jun 19 2017 19:18
Sounds good. Thanks for the prompt reply!
Paolo Di Tommaso
@pditommaso
Jun 19 2017 19:19
:+1:
Paolo Di Tommaso
@pditommaso
Jun 19 2017 20:29
Just uploaded version 0.25.0-RC4, please give it a try