Code

Release: 2.5.0#524

Code

Merged

jfy133 merged 64 commits intomasternf-core/mag:masterfrom devnf-core/mag:devCopy head branch name to clipboardOct 10, 2023

+442-181

Commits

Commits on Sep 5, 2023

• handle local kraken2 db

  gregorysprenger

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• handle local centrifuge db

  gregorysprenger

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• use busco_db and handle local and downloaded tar.gz files

  gregorysprenger

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• update information about kraken, centrifuge, and busco databases

  gregorysprenger

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Commits on Sep 15, 2023

• update parameter handling

  gregorysprenger

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• set busco_db input as a path channel

  gregorysprenger

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• handle busco_db inputs and allow for busco to auto download lineages

  gregorysprenger

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Commits on Sep 25, 2023

• Template update for nf-core/tools version 2.10

  nf-core-bot

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Commits on Sep 26, 2023

• update changelog

  jfy133

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  b2df8da

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• Merge pull request #513 from nf-core/bump-version

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  jfy133

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• Merge branch 'dev' into nf-core-template-merge-2.10

  jfy133

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• [automated] Fix linting with Prettier

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• fix dumpsoftwware hash

  jfy133

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• Comments after review

  jfy133

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• Improve TODO

  jfy133

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• Update CHANGELOG

  jfy133

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• Fix CONCOCT missing in some globs

  jfy133

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• Update CHANGELOG

  jfy133

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• Fix directory names of GUNC output to prevent overwriting

  jfy133

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• Apply suggestions from code review

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• Update CHANGELOG

  jfy133

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• Update OUTPUT docs

  jfy133

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• Merge pull request #511 from nf-core/nf-core-template-merge-2.10

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Commits on Sep 27, 2023

• Merge branch 'dev' into fix-missing-concoct-globs

  jfy133

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• Merge branch 'dev' into fix-gunc-overwriting

  jfy133

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• Update docs/output.md

  jfy133

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• Update megahit.nf

  prototaxites

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• Update CHANGELOG.md

  prototaxites

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• Merge pull request #514 from nf-core/fix-missing-concoct-globs

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• Merge branch 'dev' into fix-gunc-overwriting

  jfy133

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• Merge branch 'dev' into fix_megahit

  prototaxites

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• Merge pull request #515 from nf-core/fix-gunc-overwriting

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• Merge branch 'dev' into fix_megahit

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• Merge pull request #516 from prototaxites/fix_megahit

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Commits on Sep 28, 2023

• update centrifuge_db help text

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  gregorysprenger

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  jfy133

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• update kraken2_db help text

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  gregorysprenger

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  jfy133

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• update busco_db help text

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  gregorysprenger

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  jfy133

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  d9e7cc8

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• fix grammar error

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  gregorysprenger

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  jfy133

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Commits on Oct 3, 2023

• Correct globs and put summary in right place for Tiara

  jfy133

  committed
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• Update CHANGELOG.md

  jfy133

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Commits on Oct 4, 2023

• Update docs/output.md

  jfy133

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• Apply suggestions from code review

  jfy133

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• Merge pull request #520 from nf-core/tiara-publish-fix

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Commits on Oct 5, 2023

• space needed for when adding to p var

  gregorysprenger

  committed
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• fix busco directory handling and have consistency on channel vars

  gregorysprenger

  committed
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• harshil rule on emit lines

  gregorysprenger

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• db_name has to be the same as centrifuge filenames

  gregorysprenger

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Commits on Oct 6, 2023

• update changelog

  gregorysprenger

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  04ceb89

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• Fix nulls in bin depths

  jfy133

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  d511ebd

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• fix spelling error

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  gregorysprenger

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  jfy133

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  5cb4f41

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• use file attribute getBaseName

  gregorysprenger

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• revert back to only decompressing tar.gz files

  gregorysprenger

  committed
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• handle centrifuge and kraken db parsing

  gregorysprenger

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Commits on Oct 7, 2023

• Merge pull request #522 from nf-core/fix-null-in-depths

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Commits on Oct 8, 2023

• less verbose way of checking multiple file extensions

  gregorysprenger

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• remove view function from channel

  gregorysprenger

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• use getSimpleName file attribute

  gregorysprenger

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• update changelog

  gregorysprenger

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Commits on Oct 9, 2023

• Merge branch 'dev' into add_local_db

  gregorysprenger

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• Add depcrecateion and updated changed entries

  jfy133

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• [automated] Fix linting with Prettier

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• Merge pull request #504 from gregorysprenger/add_local_db

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  jfy133

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• Update version for release

  jfy133

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Commits on Oct 10, 2023

• Update CHANGELOG.md [skip ci]

  jfy133

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