Difference between revisions of "21th Discussion-6 Nov 2018"
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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 | + | UPDATE: Here are the [https://t.co/FecFUcOzDk slides from the talk] |
| + | and the [http://bifx-core.bio.ed.ac.uk/Bioinf-Core/zoom_1.mp4 full video] | ||
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| + | 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 | + | ** What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that? |
| + | *** Are there tools, or existing configuration files, that would make the job easier? | ||
| + | *** Any good GUIs such as can be found in Galaxy? | ||
| + | ** Resources per pipeline language? Such as YAML files for each tool? | ||
| + | *** Yes | ||
| + | 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? | ||
Latest revision as of 04:59, 13 November 2018
Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core.
UPDATE: Here are the slides from the talk and the full video
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
- What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?
- Are there tools, or existing configuration files, that would make the job easier?
- Any good GUIs such as can be found in Galaxy?
- Resources per pipeline language? Such as YAML files for each tool?
- Yes
- What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?
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?
