These are chat archives for nextflow-io/nextflow

16th
Aug 2018
Shellfishgene
@Shellfishgene
Aug 16 2018 07:48
@tbugfinder Thanks, that's useful. Yes, the help text could be a little longer, -l could also show more explanations of what the fields mean.
Phil Ewels
@ewels
Aug 16 2018 12:12
Hi @pditommaso - it looks like it's not possible to access the manifest variables from within the workflow script (main.nf). I get the error:
ERROR ~ No such variable: manifest
Is it possible to make these accessible in the same way as other variables? I'd love it if we can keep all pipeline metadata together in the manifest block:
manifest {
  name = 'nf-core/rnaseq'
  description = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
  homePage = 'https://github.com/nf-core/rnaseq'
  author = 'Phil Ewels, Rickard Hammarén'
  pipelineVersion = '1.0dev'
  mainScript = 'main.nf'
  nextflowVersion = '>=0.31.1'
}
however, we need to be able to access stuff like the pipeline version for logging. We can store it in a second variable for that purpose, but it seems a bit overkill
It'd be nice if we could just reference $manifest.pipelineVersion or whatever in the script
Phil Ewels
@ewels
Aug 16 2018 12:20
ah crap, I just found an issue where I already asked you the same thing: nextflow-io/nextflow#632
LukeGoodsell
@LukeGoodsell
Aug 16 2018 13:11
Hi all, what’s the current recommended way of passing an input file to an output channel set? Renaminging and capturing? Or is there something more elegant?
Sander Bervoets
@Biocentric
Aug 16 2018 15:27
@tbugfinder About the Salmon quant errors i'm getting. Nextflow complains about this: WARN: Process configuration syntax $processName has been deprecated -- Replace process.$quant = <value> with a process selector
Could it be that the AWS Batch does not allocate enough memory or such for quant due to the fact that it does not pass on the config parameters?
tbugfinder
@tbugfinder
Aug 16 2018 19:52
@Biocentric low memory could be an issue. Could you check the men/cpu settings within AWS Batch job definition and maybe increase those for testing ?