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[v3.0.x] Remove Hadoop dependencies#119

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seppinho merged 35 commits intov3.0.xgenepi/cloudgene:v3.0.xfrom v3.0.x-remove-hadoopgenepi/cloudgene:v3.0.x-remove-hadoopCopy head branch name to clipboardSep 20, 2023

+3,513-5,682

Commits

Commits on Aug 23, 2023

• Remove haddop support and refactor workspace

  lukfor

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  ab12ce5

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• Refactor workspace classes

  lukfor

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Commits on Sep 4, 2023

• Support s3 in Nextflow tasks

  lukfor

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  8e6bdc4

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• Fix settings and cleanup old values

  lukfor

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• Fix uploadLimit

  lukfor

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Commits on Sep 5, 2023

• Fix log files of NextflowTasks

  lukfor

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• Add reporting and improve Nextflow support

  lukfor

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  8e26679

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• Fix local workspace and downloads

  lukfor

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Commits on Sep 6, 2023

• Cleanup engine and remove seconda queue and DAG

  lukfor

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Commits on Sep 7, 2023

• Remove cloudgene-sdk, improve logging and implement reporting

  lukfor

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  9c69209

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• Refactore NextflowCommand and NextflowCollector

  lukfor

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  a2e9a8c

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• Run Nextflow jobs in workspace directory

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  d48dfe3

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• Fix missing command in report

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Commits on Sep 8, 2023

• Export environment variables when run Nextflow

  lukfor

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Commits on Sep 9, 2023

• Add global nextflow config file and add webui

  lukfor

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  b6c4c4e

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• Remove preprocessing queue

  lukfor

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• Add contact details and server url to admin panel

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  e4efab2

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• Improve application settings and environment variables

  lukfor

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  efe4b63

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• Fix issue with job in environment

  lukfor

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  ffc82ef

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• Fix issue with email settings

  lukfor

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  c1795bf

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• Add links to nextflow.log, trace and report

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  cba304f

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• Fix issue with wrong username in jobs list

  lukfor

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  53458eb

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• Add workspace to admin panel

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  096e29b

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• Fix issue with filenames in local workspace

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Commits on Sep 10, 2023

• Clean up downloads and fix logs on job restart

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Commits on Sep 11, 2023

• Remove delete temp directory on setup job to enable resume

  lukfor

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  bf4a030

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• Add label to process config

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  9bd1ee6

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• Improve Nextflow feedback rendering

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• Add job name to environment

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  11f782b

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• Set java version to 11

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Commits on Sep 12, 2023

• Remove deprecated properties from job

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Commits on Sep 13, 2023

• Remove deprectated property progress

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Commits on Sep 17, 2023

• Extended binded lists

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Commits on Sep 18, 2023

• Upload job infos to workspace

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• Support cloudgene.report.json on step level

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