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ASCC multi-assembly re-write#65

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DLBPointon wants to merge 61 commits intodevsanger-tol/ascc:devfrom dp24_version_1sanger-tol/ascc:dp24_version_1Copy head branch name to clipboard

+12,060-3,336

Commits

Commits on Nov 12, 2024

• Updates as part of Version 1 rewrite

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  4403b94

• Updates as part of Version 1 rewrite

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  4589922

• Updates as part of Version 1 rewrite

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  e2dfd3a

Commits on Nov 13, 2024

• Updates from rewrite to main repo

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  79f36bf

• Updates from rewite

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  fd29a3d

• Updating test case and CICD

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  1366293

• Updates from Eeriks docs branch

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  9bd0beb

• Roll back a couple of things

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  0a8d370

• Formatting updates

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  2c810e9

• Newline

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  6c49224

• Updates for CICD - addition of the modules.json

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  68f7521

• Updates for CICD

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• Updates for CICD

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  fdd1b02

• Updates for CICD

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  91cd465

Commits on Nov 14, 2024

• Adding a test function to parse nextflow version and resouce requirements

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  735c78a

• Adding a test function to parse nextflow version and resouce requirements

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  834ceb0

• Adding a test function to parse nextflow version and resouce requirements

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  cb574c7

• Adding a test function to parse nextflow version and resouce requirements

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  committed
  dff1b55

• Adding a test function to parse nextflow version and resouce requirements

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  committed
  6dd6867

• Adding a test function to parse nextflow version and resouce requirements

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  27b9129

• Updates

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  fd521dc

• Updates

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  0612a44

• Adding a GitHub test yaml

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  a4e87aa

Commits on Nov 15, 2024

• Pinning verison of nf-core and bug fixes

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  5a092d7

• Pinning verison of nf-core and bug fixes

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  e5024e7

Commits on Nov 18, 2024

• Update min nextflow version to test on

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  44c8bd6

Commits on Nov 20, 2024

• updates

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  cee7a3c

Commits on Nov 21, 2024

• Updating modules and fixing blast_lineage bug

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  fa27ff0

• Updating modules and fixing blast_lineage bug

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  568d701

• Fixing CI data

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  fd00d0f

• Fixing CI data

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  a89bd83

• Fixing CI data

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  048671a

• Fixing CI data

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  2334287

• Fixing CI data

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  7aac083

Commits on Nov 26, 2024

• Updating biopython+numpy images built with anaconda to biopython wo anaconda

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  302c18e

• Linting YML was broken

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  a28e957

• Pre Commit linting

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  88d7423

• Pre Commit linting

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  4f717cd

• Pre Commit linting

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  6cc000f

• Pre Commit linting

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  35703e4

• Pre Commit linting

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  62552c6

• Re-add pipeline download

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  03f6ead

• Re-add pipeline download

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  7e5f64d

• Forgot to point it to the github_testing folder

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  f5f2e92

• Forgot to point it to the github_testing folder

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  c7dd1a9

Commits on Nov 27, 2024

• Updating notes in the pipeline and removed the BTK_YAML arg from the github_test.yaml

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  5dd28da

Commits on Nov 28, 2024

• Using realpath so we don't have to pass the bam around like a wally

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  3d24a42

Commits on Nov 29, 2024

• Updates to pipeline

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  3b8d923

• Uncomment out the organellar workflow

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  0fb7342

• Lint

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  d2dbd4a

• revert blast makeblastdb to original

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  0e6d799

• Updated to fix organellar BTK issue

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  8e2ec15

Commits on Dec 2, 2024

• Removing local busco dataset call

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  b05a4a6

Commits on Dec 5, 2024

• Updates

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  e35a762

• Updating setup-nextflow from 1 to 2

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  aa241a9

Commits on Dec 9, 2024

• Updates

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  ca770c9

Commits on Dec 12, 2024

• Adding functionality for gzipped input

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  f432b42

• Adding functionality for gzipped input

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  fa7ebf2

• Updates

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  8afa3ec

• Citation for sanger-tol-btk

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  4d3f395

• Note for further updates

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  4335b1e