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LilyAnderssonLee wants to merge 108 commits intocrazy-corginf-core/taxprofiler:crazy-corgifrom devnf-core/taxprofiler:devCopy head branch name to clipboard

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Commits on Oct 8, 2024

• Template update for nf-core/tools version 3.0.0

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• Template update for nf-core/tools version 3.0.1

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• Template update for nf-core/tools version 3.0.2

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Commits on Oct 17, 2024

• resolve the conflicts

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• remove max_cpu from test.config

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Commits on Oct 18, 2024

• update schema wit new release

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• add exists:true to the sechma to check the file path

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• change db_path format back to the original value path in schema_database

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Commits on Oct 22, 2024

• update the type of run_accession into string and integer

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• Update CITATIONS.md

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• Update conf/modules.config

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• address comments from James

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• Add Lili as co-author

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Commits on Oct 24, 2024

• Fix CI to run each test separately

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• Update main.nf

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• [automated] Fix code linting

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• Fix mOTUs if/else statemetn

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• update configs and database schema

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• Merge pull request #545 from nf-core/nf-core-template-merge-3.0.2

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• Add darkmode version of metromap

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• Merge pull request #548 from nf-core/darkmode-diagram

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Commits on Oct 31, 2024

• Fix darkmode diagram

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• refactor: prepare the additional prefixes input

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Commits on Nov 5, 2024

• chore: update krakenuniq/preloadedkrakenuniq

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Commits on Nov 6, 2024

• fix: create always unique prefix

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Commits on Nov 21, 2024

• fix: make prefix unique across PE and SE

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• Update CHANGELOG.md

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• Merge pull request #549 from nf-core/darkmode-diagram

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• Merge pull request #550 from nf-core/update-krakenuniq

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Commits on Nov 22, 2024

• update nonpareil/curve

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• update CHANGELOG.md

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• Merge pull request #552 from nf-core/nonpareil_curve_update

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Commits on Nov 25, 2024

• bump the version

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• update changelog

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• Merge pull request #553 from nf-core/pre_patch_bump_v

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Commits on Nov 28, 2024

• Move the modules.config line below the base.config line

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• update configs

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• Merge pull request #556 from nf-core/patch_release_fix

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• Merge pull request #554 from nf-core/dev

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• Bump the version after patch release v1.2.1

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• Merge pull request #557 from LilyAnderssonLee/post_release_bump

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Commits on Dec 12, 2024

• Template update for nf-core/tools version 3.1.0

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• resolve the template updates conflicts

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• Update main.nf

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• update taxprofiler.nf

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Commits on Dec 17, 2024

• remove unused functions in subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf

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• remove genomes definition from schema

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• update nextflow_schema.json

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• Update nextflow.config: remove emails

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Commits on Dec 19, 2024

• update nextflow.config

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• Update docs/usage.md

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• Update nextflow.config

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• Merge pull request #558 from nf-core/nf-core-template-merge-3.1.0

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• Update centrifuge to fix CONDA bug

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• Merge branch 'dev' into fix-centrifuge-conda

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• Update CHANGELOG.md

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• Merge pull request #561 from nf-core/fix-centrifuge-conda

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• Bump the version before the patch release v.1.2.2

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• correct the format

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• reformat the multiqc_config.yml

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Commits on Dec 20, 2024

• update CHANGELOG.md

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• Merge pull request #562 from nf-core/pre-release_vbump

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• Template update for nf-core/tools version 3.1.0

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• Template update for nf-core/tools version 3.1.1

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Commits on Jan 2, 2025

• resolve the conflicts

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• correct main branch into master

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• correct the formate

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• update CITATIONS

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• prettier modules.json

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• Update the CHANGELOG.md

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Commits on Jan 3, 2025

• Update nextflow_schema.json

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• Merge pull request #565 from nf-core/nf-core-template-merge-3.1.1

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Commits on Jan 9, 2025

• Test fix for downloading

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• Check if the fix works when opening PR against dev

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• Remove the dev from branches

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• Test new fix

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• Merge pull request #566 from sofstam/download_pipeline_fix

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Commits on Jan 14, 2025

• Use profile variable instead of hardcoding docker

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• Merge pull request #567 from nf-core/fix-release-tests-for-condasingularity

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• Update CHANGELOG.md

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• Post-release bump version

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• Update CHANGELOG.md

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• Prettier

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• Merge branch 'bump_version_1.3.0' of https://github.com/nf-core/taxprofiler into bump_version_1.3.0

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• [automated] Fix code linting

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• Merge pull request #568 from nf-core/bump_version_1.3.0

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Commits on Jan 20, 2025

• Template update for nf-core/tools version 3.1.2

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• Merge branch 'dev' into nf-core-template-merge-3.1.2

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• Update nextflow.config

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• Update zenodo

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• Apply suggestions from code review

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• Merge pull request #569 from nf-core/nf-core-template-merge-3.1.2

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