These are chat archives for nextflow-io/nextflow

18th
Feb 2018
Venkat Malladi
@vsmalladi
Feb 18 2018 01:17
@vsoch so you ideally want a container that is just nextflow that can spin up different containers for each process that runs those applications?
Vanessasaurus
@vsoch
Feb 18 2018 02:13
I want a container that has different entrypoints that a scientist wants to run (e.g., samtools might be one) and then to run it using nextflow, whatever that happens to mean! I first tried installing with the wget and bash script and the executable "nextflow" appeared but it also gave me an error message. Next I tried pulling the docker nextflow/nextflow into a singularity image, and then tun against my docker container (with the samtools) but it gave the issues I showed in the link. I haven't ever actually delved into doing anything substantial with it so I'm not even sure if I am thinking of how it works the right way.
Venkat Malladi
@vsmalladi
Feb 18 2018 02:17
I would defer to @pditommaso. An example I have found that might be helpful is https://github.com/c-guzman/cipher-workflow-platform
Vanessasaurus
@vsoch
Feb 18 2018 02:18
ah thank you, I will take a look! There is definitely no rush, I'm having dinner and won't work on this any time soon :)
Vanessasaurus
@vsoch
Feb 18 2018 20:23
okay, so after about 8 hours on this today, I have not been able to get it to work. I've been able to show running using scif, but failed with all aspects of nextflow. I had wanted to write this up and give attention to the three technologies, but it looks like nextflow is going to be left out, unless someone can help me to get it working. I have documented everything here https://github.com/vsoch/rnatoy.scif
the last thing I'll do (what's another hour the weekend is gone anyway) is added the singularity commands, they are a lot cleaner than docker given no need for special binds
Vanessasaurus
@vsoch
Feb 18 2018 20:54
okay, singularity example is done, for nextflow I give up https://github.com/vsoch/rnatoy.scif