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Optional alignment subworkflow#83

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priyanka-surana merged 32 commits intoreleasesanger-tol/blobtoolkit:releasefrom alignmentsanger-tol/blobtoolkit:alignmentCopy head branch name to clipboardOct 18, 2023

+1,007-143

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Commits on Jul 19, 2023

• Use the path under resources/nextflow

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Commits on Aug 1, 2023

• Download the databases to make it work on GitHub

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• This should be a S3 path too

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• Need to use the CRAM files from S3 too

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• quay.io os now the default registry

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• quay.io os now the default registry

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• This file is changed on purpose

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Commits on Aug 4, 2023

• Override the BUSCO settings in the test profile

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• Our new convention is use per-pipeline directories under pipeline_info/

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Commits on Aug 14, 2023

• Latest nomenclature

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• The minimum version is actually 22.10 (tested on GitHub)

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• Use the latest version of the Tower action

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• Final version of the BUSCO database

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Commits on Aug 16, 2023

• Update sanger_test.yml

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• Update sanger_test_full.yml

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• Update sanger_test.yml

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• Update sanger_test_full.yml update workflow name

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Commits on Aug 18, 2023

• New tolsoft details

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• Fixed the repository name

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Commits on Sep 17, 2023

• adding alignment modules

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• created alignment subworkflow from template

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• minimap alignment subworkflow

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• update modules

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• all tests work

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• update nextflow schema

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• forgot to add busco diff

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Commits on Sep 18, 2023

• Moved all the test data to the S3 bucket

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Commits on Sep 26, 2023

• Merge pull request #82 from sanger-tol/test_ci

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Commits on Sep 27, 2023

• review comments

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• prettier fix

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• prepare genome subworkflow

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Commits on Oct 18, 2023

• Merge pull request #84 from sanger-tol/prepare_genome

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