These are chat archives for nextflow-io/nextflow

27th
Nov 2018
Maxime HEBRARD
@mhebrard
Nov 27 2018 01:51
@micans oh yes, toList() is doing what I want ! thanks
KochTobi
@KochTobi
Nov 27 2018 13:25
Hi there, is it possible to assign custom AWS tags to all instances started by AWS Batch via nextflow based on process name or a run specific custom identifier (param) ? And will there be one instance per process or are multiple processes bundeled?
Maxime Garcia
@MaxUlysse
Nov 27 2018 13:27
I like that idea
Paolo Di Tommaso
@pditommaso
Nov 27 2018 13:27
open an feature request for that
KochTobi
@KochTobi
Nov 27 2018 14:18

@pditommaso done

#948

Robin
@rduque1
Nov 27 2018 14:35
Hi, is it possible to run nextflow with private docker containers?
Kevin Sayers
@KevinSayers
Nov 27 2018 14:51
https://www.nextflow.io/docs/latest/config.html#scope-docker the registry parameter can be used to specify a private repository.
Thomas Van Parys
@thpar
Nov 27 2018 15:08
is there a way to set sub-parameters from the commandline? Like you can set params.mytest as --mytest foo, could you set params.mytest.bar in some way?
Paolo Di Tommaso
@pditommaso
Nov 27 2018 15:09
nope, use the config file
Thomas Van Parys
@thpar
Nov 27 2018 15:14
Ok, tnx!
micans
@micans
Nov 27 2018 16:57
@pditommaso I just started a pipeline with 30K samples. In the final merge step this will mean I will have 30K files linked into a process work directory. I wonder if it could be a new channel feature to collect a single file that contains, per line, the files output by the channel. Something like collectLinks(). An application in the script section can then be given this file.
micans
@micans
Nov 27 2018 17:18
For these 30K samples the -ansi option is :rocket:
Paolo Di Tommaso
@pditommaso
Nov 27 2018 17:22
nice
I wonder if it could be a new channel feature to collect a single file that contains, per line, the files output by the channel.
you can do with collectFile { file -> file.toString() }
micans
@micans
Nov 27 2018 17:23
heeeeeyyyyyyyyyy!
Paolo Di Tommaso
@pditommaso
Nov 27 2018 17:25
if it works, add it as a new pattern here :wink:
micans
@micans
Nov 27 2018 17:26
That is very cool. I will test this ... need to rewrite a script a bit first.
Paolo Di Tommaso
@pditommaso
Nov 27 2018 17:26
:ok_hand:
micans
@micans
Nov 27 2018 17:26
Thanks!
Paolo Di Tommaso
@pditommaso
Nov 27 2018 17:26
welcome