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v2.0.2: Clean-up#96

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marinak-ebi merged 37 commits intomastermpi2/impc_stats_pipeline:masterfrom devmpi2/impc_stats_pipeline:devCopy head branch name to clipboardNov 11, 2024

+214-36,532

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Commits on Jun 24, 2024

• Create scripts directory with helper scripts

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• Correct a typo

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Commits on Jul 16, 2024

• Merge pull request #81 from mpi2/scripts

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Commits on Jul 18, 2024

• Add script run_pipeline.sh that execute stats and annotation pipeline

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Commits on Jul 19, 2024

• Fix errors

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• Add messages

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• Update README.md with new running instructions

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Commits on Jul 23, 2024

• Merge pull request #85 from mpi2/running-script

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• Replace miniparquet with arrow

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• Install dependencies set to TRUE

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• Reorder packages

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• Add dependency update parameter

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• Add documentation to recreate environment

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• Convert the dependencies argument to logical type

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• Add third parameter to the UpdatePackagesFromGithub in the running script

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• Add rwebhdfs library to the description

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• Add installation rwebhdfs in UpdatePackagesFromGithub.R

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Commits on Jul 26, 2024

• Merge pull request #82 from mpi2/new-env

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• Update LICENSE copyright data

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• Merge pull request #86 from mpi2/license

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• Remove gross morphology commented code

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• Remove IMPC_statspipelinePostProcess function that is not in use

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• Remove splitIndexFileIntoPiecesForPvalueExtraction function that is not in use

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• Remove editfile function that is not in use

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• Remove ClearReportsAfterCreation function that is not in use

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• Remove HadoopReTransfer function that is not in use

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• Remove HadoopReTransferSCP function that is not in use

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• Clean up README.md from functions that are not in use

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• Remove ExtractPVals.R

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• Remove ExtractPValsPhenStat.R

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• Remove unnessasary step from README.md

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Commits on Aug 9, 2024

• Merge pull request #87 from mpi2/clean-up

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• Remove EquationMap.conf

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• Remove getEquation function

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• Refactor mainAgeing function

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• Remove updateEquationMap function

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Commits on Oct 8, 2024

• Merge pull request #89 from mpi2/remove-equation

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