Difference between revisions of "21th Discussion-6 Nov 2018"
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(Comments on points to clarify before talk (by Alex Peltzer)) |
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Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core. | Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core. | ||
| − | After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core. This will be on November 6th, 3 PM GMT. Details on how this will occur are being | + | After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core. This will be on November 6th, 3 PM GMT. Details on how this will occur are being finalized but I would invite everyone to submit any questions ahead of the demo so we can all get the most out of it. |
Please add your questions below: | Please add your questions below: | ||
| − | * How to configure a pipeline for all users | + | * How to configure a pipeline for all users? |
| − | * How/where is | + | * How/where is the best location to store pipelines and make them accessible for users? |
| − | * How bad are the docker vulnerabilities | + | * How bad are the docker vulnerabilities? |
| − | * How to configure | + | * How to configure Dockerized pipelines properly? |
| − | * How to convert | + | * How to convert Docker pipelines to singularity (with and without AWS)? |
* Easiest pipelines to create from scratch | * Easiest pipelines to create from scratch | ||
| − | * Resources per pipeline language? Such as | + | a What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that? |
| + | * Resources per pipeline language? Such as YAML files for each tool? | ||
| + | b Not sure what you mean with this - do you mean how we define dependencies per pipeline? | ||
* Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs? | * Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs? | ||
Revision as of 11:33, 3 November 2018
Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core.
After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core. This will be on November 6th, 3 PM GMT. Details on how this will occur are being finalized but I would invite everyone to submit any questions ahead of the demo so we can all get the most out of it.
Please add your questions below:
- How to configure a pipeline for all users?
- How/where is the best location to store pipelines and make them accessible for users?
- How bad are the docker vulnerabilities?
- How to configure Dockerized pipelines properly?
- How to convert Docker pipelines to singularity (with and without AWS)?
- Easiest pipelines to create from scratch
a What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?
- Resources per pipeline language? Such as YAML files for each tool?
b Not sure what you mean with this - do you mean how we define dependencies per pipeline?
- Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?
