These are chat archives for nextflow-io/nextflow

11th
Nov 2017
John C Earls
@jcearls_twitter
Nov 11 2017 22:22 UTC

Hello, I am just getting started with this tool and it appears that nextflow is not interacting w/ docker

I tried working from https://github.com/nextflow-io/examples and running

nextflow run fasta_record.nf

Which is the first example that really needs a docker image fails.

the failure is the blastp package, that is not installed on the host.

nextflow appears to just ignore the docker commands, whether I add the container to a process, the config file or --with-docker
It doesn't throw an error or anything when I give it a bad docker image name.
Paolo Di Tommaso
@pditommaso
Nov 11 2017 22:24 UTC
-with-docker not --with-docker
John C Earls
@jcearls_twitter
Nov 11 2017 22:26 UTC
I figured it was something stupid
thank you
Paolo Di Tommaso
@pditommaso
Nov 11 2017 22:26 UTC
:+1:
John C Earls
@jcearls_twitter
Nov 11 2017 22:28 UTC
Is there an equally silly reason why it is not recognizing nextflow.config?
Paolo Di Tommaso
@pditommaso
Nov 11 2017 22:30 UTC
nextflow.config must be located in the launch directory
John C Earls
@jcearls_twitter
Nov 11 2017 22:31 UTC
and
In the latter case the examples below marked with a * character need to be run adding the -with-docker command line option.
from the tutorial
sorry
been a long day
Paolo Di Tommaso
@pditommaso
Nov 11 2017 22:31 UTC
no pb
John C Earls
@jcearls_twitter
Nov 11 2017 22:40 UTC
If I try to create an aws cloud using nextflow, do I need to use an ami with slurm or sge already set up and configured or does nextflow manage that?
Paolo Di Tommaso
@pditommaso
Nov 11 2017 22:41 UTC
NF has it's own clustering engine, it doesn't require slurm or sge
John C Earls
@jcearls_twitter
Nov 11 2017 22:41 UTC
nice
Looks like a very cool tool
Paolo Di Tommaso
@pditommaso
Nov 11 2017 22:42 UTC
so people say :)