New deployment strategy for containers and ngi_pipeline support for sarek v2.6.1

General changes

Containers are now added to a directory outside the versioned deployment directories: /lupus/ngi/containers/. The reason for this is to avoid downloading all containers to every environment version. Using this approach makes deployment faster and make the deployment take up less space.
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The following software are no longer deployed:

• arteria-siswrap
• neutronstar
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Changes per role

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• MultiQC

  • Updated to v1.9
  • MegaQC details added to Uppsala's config
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• nf-core

  • Added nfcore/viralrecon
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• sarek

  • Updated to v.2.6.1
  • The apply_recalibration script is now adapted for sarek and managed in this role (previously in ngi_pipeline repo)

• ngi_pipeline

  • Support for Sarek v2.6.1 added
  • Updated Charon timeout limit
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• anaconda

  • New python 3.8 environment added (called NGI_py3)
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• ngi_reports

  • Updated version that runs on py3 (py2 no longer supported) and dependency to pandoc has been dropped
  • No longer used by Uppsala
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• nextflow

  • Uppsala's nextflow config do no longer specify to run MultiQC processes locally
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• TACA

  • Updated version
  • Configs added for staging sarek data