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Release PR for 2.1.0#456

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Commits on Sep 5, 2024

• Post-release version bump

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• Merge pull request #416 from nf-core/post-release-bump

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• 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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• Update antismash, argnorm, rgi citations

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Commits on Oct 23, 2024

• Merge branch 'dev' into nf-core-template-merge-3.0.2

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• Skip igenomes and fastqc becuase no reads nor reference genome

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• Remove max_ params for all other profiles

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• Fix linting errors

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• Fix schema linting errors

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• Update all modules

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• Remove check_max and max_ parameters

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• Update missing module

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• Fix schema

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Commits on Oct 30, 2024

• Merge pull request #422 from nf-core/update-citations

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Commits on Nov 19, 2024

• Update .nf-core.yml

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Commits on Dec 3, 2024

• update the amp db download script

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• update to use ampcombi 2.0.1

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• fix parametrs

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• fix schema values

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Commits on Dec 4, 2024

• update the docs

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• [automated] Fix code linting

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• update nextflow.config

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Commits on Dec 5, 2024

• install interproscan in funcscan

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• add module in modules.json

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Commits on Dec 9, 2024

• start adding interproscan_amp functionality

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• add citation

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• update dynamic optional parameter path

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Commits on Dec 11, 2024

• remove dynamik ext.arg

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Commits on Dec 12, 2024

• Template update for nf-core/tools version 3.1.0

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• update ampcombi2 2.0.1

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Commits on Dec 16, 2024

• fix the ampcombi inputs

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• fix error strategy

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• Merge pull request #427 from nf-core/add_ampcombi_2.0.1

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Commits on Dec 18, 2024

• Add AMPcombi to 2.0.1

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• Add darkmode diagram

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• Merge branch 'nf-core-template-merge-3.0.2' of github.com:nf-core/funcscan into nf-core-template-merge-3.0.2

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• Add contributor information

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• Update snapshots due to new macrel and ampcombi versions

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• Merge branch 'dev' into nf-core-template-merge-3.0.2

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• Fix precommit and missing prokka snapshot

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• Fix ARG tool variability

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• Merge pull request #421 from nf-core/nf-core-template-merge-3.0.2

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• Merge branch 'dev' into nf-core-template-merge-3.1.0

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Commits on Dec 19, 2024

• Fix tests

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• Update subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf

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• Update several modules

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• Update nextflow.config

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• Merge pull request #429 from nf-core/nf-core-template-merge-3.1.0

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• Update CHANGELOG.md

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• Update snapshot (due to CARD database update)

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• Merge pull request #430 from nf-core/update-rgi

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Commits on Dec 20, 2024

• Add mmseqs patches, fix snapshots of ampir and deepbgc

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• Merge branch 'dev' into update-modules

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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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• Fix ampir nf.test + increase antismashdownloaddatabases time

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Commits on Dec 23, 2024

• Add compressed flag as ext.args to mmseqs modules

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Commits on Jan 6, 2025

• Merge remote-tracking branch 'origin/dev' into add_interproscan_to_amp

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Commits on Jan 8, 2025

• remove comments and fix Interproscan subworkflow

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• [automated] Fix code linting

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• fix linting issues

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• fix ampcombi when only one file passes parsetables

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Commits on Jan 9, 2025

• fix ampcombi2 wo interproscan

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• clean up comments

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Commits on Jan 10, 2025

• fix merge taxonomy scripts and outputs

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• fix ARG TABIX output file name

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• fix output declaration for args

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• update nf tests

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• Merge branch 'dev' into nf-core-template-merge-3.1.1

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• Fix PR request template

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• Apply suggestions from code review

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Commits on Jan 15, 2025

• Apply suggestions from code review

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• Update mmseqs to v16, update multiqc to v 1.26 [skip ci]

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• Update changelog [skip ci]

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• Patch mmseqs/createtsv

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• Merge pull request #433 from nf-core/nf-core-template-merge-3.1.1

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• Merge pull request #435 from nf-core/fix_taxonomy_files

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• Add logic to skip cardannotation

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• Remove mmseqs patches, update prokka module to include nf-test

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• Fix logic of cardannotation execution

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Commits on Jan 16, 2025

• Update mmseqs (update snapshot of createdb), undo prokka change

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• Update something (to trigger CI tests)

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• Patch mmseqs modules to version 15 instead of 16

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• Merge pull request #437 from nf-core/fix-rgi-db-name-issue

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Commits on Jan 17, 2025

• Update all mmseqs modules to v16, change --search-type default to have taxonomy workflow succeed

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Commits on Jan 19, 2025

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Commits on Jan 20, 2025

• Template update for nf-core/tools version 3.1.2

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Commits on Jan 21, 2025

• Update all MMseqs modules to v17, update changelog

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• Change mmseqs searchtype default value back to 2

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• Merge branch 'update-modules' of github.com:nf-core/funcscan into update-modules

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• Update seqkit

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• Fix nf-test

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• Re-add trace_report_suffix param in schema

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

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• Fix linting

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• Merge pull request #438 from nf-core/nf-core-template-merge-3.1.2

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• Template update for nf-core/tools version 3.2.0

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• Merge branch 'dev' into nf-core-template-merge-3.2.0

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• Update antismash modules + changelog

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• Apply suggestions from code review; fix linting warning (rocrate)

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