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nf-core/mag 3.2.0 release PR#699

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jfy133 merged 126 commits intomasternf-core/mag:masterfrom devnf-core/mag:devCopy head branch name to clipboardOct 27, 2024

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Commits on Sep 9, 2024

• Replace local spades modules with official nf-core version (missing fix CPU trick)

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• Update CHANGELOG.md

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Commits on Sep 10, 2024

• Fix output docs

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• Make sure warnings log also gets a prefix

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• Merge branch 'dev' into bump-metaspades

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Commits on Sep 12, 2024

• Fix a syntax error (Ben made me do it)

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Commits on Sep 20, 2024

• Added modules porechop/abi and chopper for QC of long reads

  

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• Move long read preprocessing into subworkflow, and swapping porechop module to porechop/abi

  

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• Remove module import from main workflow, and add PORECHOP_ABI in conf/modules.config

  

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• Switch local MEGAHIT to official nf-core one

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• Fix wrongly set branch

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• Merge branch 'dev' into bump-metaspades

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• Fix linting

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Commits on Sep 24, 2024

• Exchange local filtlong module to nf-core/filtlong

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• Add filtlong and porechop logs to multiqc

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• Added --longread_preprocessing_tools parameters, to let user specify long read preprocessing tools. Currently only has the option to specify porechop_abi, but I decided this is a nice solution for …

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Commits on Sep 25, 2024

• Merge branch 'dev' into move_lr_qc

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• Update modules/nf-core/filtlong/main.nf

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Commits on Sep 30, 2024

• make subworkflow name more verbose

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• make --longread_adaptertrimming_tool as enum porechop or porechop_abi

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• Make prefix for porechop/porechop-abi more verbose

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• lint

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Commits on Oct 1, 2024

• Change default search pattern for filtlong.log files for the filtlongmodule in multiqc

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Commits on Oct 3, 2024

• Update CHANGELOG.md

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• Update CHANGELOG.md

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• Update nextflow_schema.json

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• Update conf/modules.config

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• Update conf/modules.config

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• Update conf/modules.config

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• Update nextflow_schema.json

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• Update nextflow.config

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• Update subworkflows/local/longread_preprocessing.nf

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• Update subworkflows/local/longread_preprocessing.nf

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• Update subworkflows/local/longread_preprocessing.nf

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• Merge branch 'dev' into move_lr_qc

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• Merge branch 'dev' into bump-metaspades

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• Linting fix

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• make porechop-abi default long read adapter trimming tool

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• Replace assembler single-use fix-cpu functions with single line definitions

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• Ensure checkmax is still used

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• Specify also module changes

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Commits on Oct 4, 2024

• Fix changelog

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• Fix porechop_abi pattern in modules.config

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• Merge branch 'dev' into move_lr_qc

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• remove chopper citation for now

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• Lets see if SPAdes now works with fusion with the new container...

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• Post-release version bump

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• retrigger checks

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• Merge pull request #682 from nf-core/post-3.10-version-bump

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• Merge branch 'dev' into move_lr_qc

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Commits on Oct 8, 2024

• Fix version number in manifest

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• Template update for nf-core/tools version 3.0.0

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Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

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Commits on Oct 11, 2024

• Apply suggestions from code review

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• Apply suggestions from code review

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• Add previouysly undocumented output files to docs

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• [automated] Fix code linting

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• Merge pull request #674 from muabnezor/move_lr_qc

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• Template update for nf-core/tools version 3.0.2

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• output multiple depth files

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• accept multiple depth files

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• update CHANGELOG

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• nf-core modules patch

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• nf-core modules patch now for modules.json

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• pull from upstream and merge conflicts

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Commits on Oct 14, 2024

• publish summary and abundance files in results

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• use sample names for MaxBin2 abund

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• force install latest MaxBin2 module

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Commits on Oct 16, 2024

• Update CHANGELOG.md

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

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• Remove unused parameters

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• Comment out unusued tempalte parmaeter (renaming), and remove a duplicate entry in schema

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• Fix yaml indentation

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• Remove nonexistant section

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• Remove unused aprameter

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Commits on Oct 17, 2024

• Remove reference to max_* params and fix input schema

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• Remoce references to check_max()

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• REplace custom check_<assembly>_cpus functions

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Commits on Oct 18, 2024

• Merge pull request #690 from d4straub/fix-maxbin2-multiabund

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Commits on Oct 21, 2024

• update prodigal to helpfully not compress symlinks by having more specific pigz suffxies

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• Update CHANGELOG

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• Merge branch 'dev' into fix-prodigal-pigz

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• [automated] Fix code linting

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• Merge pull request #698 from nf-core/fix-prodigal-pigz

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• Update schema, fix empty list in tag names, fix missing parameter default

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• Fix gtdbtk default value incompatibility

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• Fix check for group column in input

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• Remove misleading error messages and allow more string types in run column

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• Use correct input for assembly input and improve schema

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• Use more workable Zenodo link for CheckM database

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• Sync nextflow schema with nextflow.config

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• Update to Zenodo URL also in test config

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Commits on Oct 22, 2024

• Change pplacer paramter to integer and fix useram default to boolean default

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• Fix citations indentitation

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• Fix GTDBTk Url in schema

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• Merge branch 'dev' into bump-metaspades

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• Update CHANGELOG

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• Merge pull request #695 from nf-core/nf-core-template-merge-3.0.2-manual

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• Merge branch 'dev' into bump-metaspades

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• Make sure meta mode is executed with the new module

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• Fix linting

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• Remove a TODO

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• Add MEGAHIT prefix to ensure MEGAHIT at the beginning of the input file name.

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• Re-add memory explicit parameter to MEGAHIT module (inbuilt into SPAdes module)

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• Re-add MEGAHIT memory

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• Use HTTPS URL for megahit container

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• Merge pull request #666 from nf-core/bump-metaspades

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• Bump version

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• Update workflow diagram

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• Merge pull request #700 from nf-core/bump-version

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Commits on Oct 24, 2024

• Fix conda environment specification to match container of sub-dependencies

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• Add darkmode diagram

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• Typo fix for the light mode

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• Soften white

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• Merge pull request #703 from nf-core/darkmode-diagram

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• Fix full test manual trigger following nf-core/methylseq@d7578f0#diff-2a52eee8221e07d380971fc23f7f5150f1ceffcf36455d27033ce79f9818c636R28

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• Merge pull request #704 from nf-core/jfy133-patch-1

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Commits on Oct 25, 2024

• Always run in --meta mode

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• Update conf/modules.config

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• Merge pull request #705 from nf-core/always-meta-parameter-metaspades

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• Harshil alignment

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Commits on Oct 26, 2024

• Update conf/test_full.config

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• Update workflows/mag.nf

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• Update .nf-core.yml

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Commits on Oct 27, 2024

• Update CHANGELOG.md

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