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Database cleanup pipeline#964

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nwillhoft wants to merge 20 commits intoEnsembl:release/mvpEnsembl/ensembl-production:release/mvpfrom nwillhoft:feature/db_cleanup_pipelinenwillhoft/ensembl-production:feature/db_cleanup_pipelineCopy head branch name to clipboard

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Commits on Feb 6, 2025

• Initial commit of db cleanup pipeline

  nwillhoft

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  d32a653

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• Rename nf file

  nwillhoft

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  6ee16cd

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• Update print outs in log info

  nwillhoft

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  5884bb9

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• Move DB_COPY_SUBMIT process to module file

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  7126e51

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• Move MONITOR_DB_COPY process to module file

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  4f791e9

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• Move GENERATE_SQL process to module file

  nwillhoft

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  7c7e1f9

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• Move COMPRESS_FILE process to module file. Update path for resulting output.

  nwillhoft

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  09bb5e0

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• No longer publish intermediate sql files

  nwillhoft

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  707231d

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• Rename main nextflow script. Follow Ensembl nextflow dir structure protocol.

  nwillhoft

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  f680105

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• Use nf-schema for parameter validation and help info

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  5db2b86

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• Add process to clear up temp database

  nwillhoft

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  30c01ff

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• Remove column stats option as no longer needed

  nwillhoft

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  398dd4c

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• Require db admin user and password for dropping a db

  nwillhoft

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  1e369bb

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• Fix drop db process with extra space and simplify drop statement

  nwillhoft

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  24b334d

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• Move CLEANUP_TMP_DB process to module file

  nwillhoft

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  4904f6b

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• Add process to drop source db when requested

  nwillhoft

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  e6fe3af

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• Remove redundant check

  nwillhoft

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  b316a81

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• Add prints for info

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  16f3969

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• Correct string type to boolean

  nwillhoft

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  323fcf9

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• Move DROP_SOURCE_DB process to module file

  nwillhoft

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  4bcb3db

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