These are chat archives for nextflow-io/nextflow

9th
Aug 2018
haidianfarmer
@haidianfarmer
Aug 09 2018 07:27
Hello everyone, I have a problem about profiles config. In the nextflow documentation the profiles have 3 parts(standard cluster and cloud) I don't understand the function of these parts like these 3.
Kevin Sayers
@KevinSayers
Aug 09 2018 07:33
@haidianfarmer those are just three example profiles, each profile specifying different executors and associated parameters.
haidianfarmer
@haidianfarmer
Aug 09 2018 07:48
@KevinSayers thank you. And what is the way that links the profile with the pipeline. For example the first kind profile included docker enabled:false and another profile included docker enabled:true. I don't understand when the different profile will work in different time. that maybe mean I haven't found the relationship between different profiles and different condition. Sorry for my so bad English.
Paolo Di Tommaso
@pditommaso
Aug 09 2018 08:19
A profile is a set of configuration attributes that can be activated/chosen when launching a pipeline execution by using the -profile command line option.
haidianfarmer
@haidianfarmer
Aug 09 2018 08:23
@pditommaso Thank you very much. What is the way that controls when the profile activates and when the profile not activate.
Paolo Di Tommaso
@pditommaso
Aug 09 2018 08:23
using the -profile command line option.
nextflow run <script> -profile <name>
makes sense ?
haidianfarmer
@haidianfarmer
Aug 09 2018 08:29
@pditommaso yes! thank you!
micans
@micans
Aug 09 2018 09:22
@pditommaso on my toy example the sample-split-subsample-join feature with groupKey(key, files.size()) works beautifully. I have a (second) use case when we have large batches of files to archive using tar; I will try that next. I'm very excited about it! (The first use case is more intricate for me to implement as the merging step is more complicated).
LukeGoodsell
@LukeGoodsell
Aug 09 2018 09:48
Is there a rationale behind why Channel.set(…) and Channel.into(…) aren’t combined into a single operator that puts channel items into one or more channels? IMHO it’d be more intuitive that way.
Paolo Di Tommaso
@pditommaso
Aug 09 2018 13:05
@micans please report your feedback in the relative issue nextflow-io/nextflow#796
thanks!
@LukeGoodsell the set it's a mere binding of the var name in the global scope
into instead need to create a copy of the channels
LukeGoodsell
@LukeGoodsell
Aug 09 2018 13:23
I see. In that case I think it’d be more intuitive if there was a single operator that would use set when 1 channel is supplied, and into when more than 1 channel is supplied. That way, as the code changes, you don’t have to remember to change between the two operators as the number of channels changes. Shall I raise an issue?
Paolo Di Tommaso
@pditommaso
Aug 09 2018 13:44
make sense
Shall I raise an issue?
yes please
micans
@micans
Aug 09 2018 14:30
@pditommaso will do :+1: (may take a few days)
Paolo Di Tommaso
@pditommaso
Aug 09 2018 14:32
no hurry, on holiday since tomorrow :satisfied:
micans
@micans
Aug 09 2018 16:22
Enjoy!