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EBI nf-core config #2

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priyanka-surana opened this issue May 31, 2023 · 3 comments
Open

EBI nf-core config #2

priyanka-surana opened this issue May 31, 2023 · 3 comments
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challenge Submitted community challenges configuration Nextflow configuration settings enhancement New feature or request help wanted Extra attention is needed

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@priyanka-surana
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priyanka-surana commented May 31, 2023 •
edited by likhitha-surapaneni
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Details below:
@priyanka-surana priyanka-surana added enhancement New feature or request help wanted Extra attention is needed challenge Submitted community challenges configuration Nextflow configuration settings labels May 31, 2023
@priyanka-surana priyanka-surana changed the title EBI nf-core configs EBI nf-core config May 31, 2023
@nuno-agostinho
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nuno-agostinho commented Jun 13, 2023 •
edited by likhitha-surapaneni
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To include in the config:

  • Add configuration for LSF/SLURM/cloud (mind job limits?)
  • Support for the LSF/SLURM queues in Codon
  • Singularity profile
  • Default options for trace, dag, timeline and report?
  • Generic environment variables using env
  • Global variables/parameters to define (such as default directories: scratch, software, production, research)
  • Default temporary directory?
  • GPU support
  • Generic errorStrategy (example)
  • Add a manifest (example)
  • Modularisation if possible using includeConfig
  • Option to enable notification

To discuss:

  • Should we create a unique profile for each option? This would allow to choose which profiles to run in Nextflow, such as -profile lsf,singularity,gpu
  • Create a README/tutorial:
    • Simple commands on how to use Nextflow and the EBI nf-core config in Codon
    • How to run a Nextflow main job (using tmux/screen or as a LSF/SLURM job itself)
    • How to use a custom config on top of the EBI config
    • How to optimise Nextflow
    • How to cleanup after Nextflow (nextflow clean or manual steps)
    • Cleanup for temporary directories
    • Further resources / help / contact
  • In which directory to put the EBI config? Who would have write permissions?
  • Add all information to Confluence or embl.service-now.com?

More information:

@likhitha-surapaneni likhitha-surapaneni removed their assignment Jun 15, 2023
@biomadeira
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We have already made good progress on this, but looking forward to continuing working on it.
See https://github.com/biomadeira/EBI-nextflow-config

@likhitha-surapaneni
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It was a great start @biomadeira , thank you to everyone who has participated! Looking forward to continue the work.

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@biomadeira @nuno-agostinho @likhitha-surapaneni @priyanka-surana