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v1.2 - Bouncy Basenji Release PR#525

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LilyAnderssonLee merged 200 commits intomasternf-core/taxprofiler:masterfrom devnf-core/taxprofiler:devCopy head branch name to clipboardOct 3, 2024

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Commits on Nov 9, 2023

• Install module

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Commits on Nov 10, 2023

• Merge pull request #416 from nf-core/dev

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• Add get it working, add to tests, update docs/images/citations

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Commits on Nov 13, 2023

• Fix groovy semantic errors

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• update gitignore to ignore nf-test

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• Revert "update gitignore to ignore nf-test"

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Commits on Nov 15, 2023

• Fix nonpareil args across all tests

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Commits on Nov 30, 2023

• Add nonpareil

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• Minor linting

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• Fix channel emission

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• Fix module linting

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• Add nonpareil to valid MultiQC entries

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• Final linting

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• [automated] Fix linting with Prettier

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• Apply suggestions from code review

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• Merge pull request #417 from nf-core/add-nonpareil

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Commits on Jan 12, 2024

• Merge branch 'dev' into bouncy-basenji

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Commits on Jan 25, 2024

• Merge dev into bouncy-basenji

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• Fix prettier

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• Remove merge marker

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Commits on Feb 8, 2024

• Merge branch 'bouncy-basenji' into fix-merge-conflict

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• Merge pull request #448 from nf-core/fix-merge-conflict

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Commits on Mar 14, 2024

• Merge dev into bouncy-basenji

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Commits on Mar 15, 2024

• Merge pull request #455 from LilyAnderssonLee/bouncy-basenji

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Commits on Mar 18, 2024

• update the nanopore and fasta input channel

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Commits on Mar 19, 2024

• Merge branch 'nf-core:master' into fix-validation

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• add fallback to download pipeline workflow

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• update nf-validation

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Commits on Mar 20, 2024

• Update workflows/taxprofiler.nf

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• Update taxprofiler.nf

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• Disable the save of kaiju2krona txt output

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Commits on Mar 21, 2024

• Merge pull request #458 from LilyAnderssonLee/fix-validation

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Commits on Apr 8, 2024

• add db_type feature into database

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• Merge branch 'merge_dev_into_bouncy' of github.com:LilyAnderssonLee/taxprofiler into LilyAnderssonLee-merge_dev_into_bouncy

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• Merge branch 'bouncy-basenji' into LilyAnderssonLee-merge_dev_into_bouncy

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Commits on Apr 11, 2024

• Merge pull request #467 from nf-core/LilyAnderssonLee-merge_dev_into_bouncy

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• update bouncy-basenji branch

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• fix the merge conflicts

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• Add missing information after fixing the merge conflicts.

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• format config files

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• update CHANGELOG.md

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• Enable downloading the results of failed tests for debugging

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• Update ci.yml

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• Update CHANGELOG.md

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Commits on Jun 11, 2024

• Merge branch 'dev' into bouncy-basenji

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• Merge branch 'bouncy-basenji' of github.com:nf-core/taxprofiler into bouncy-basenji

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• Add nonpareil to testing

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Commits on Jun 13, 2024

• combine reads and db by db_type

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• Merge branch 'bouncy-basenji' into add_db_type

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• Update ci.yml

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Commits on Jun 14, 2024

• Update profiling.nf

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Commits on Jun 18, 2024

• seperate db_type short,long(both) by semicolon

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• replace comma as semicolon in db_type

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Commits on Jun 20, 2024

• Make database splitting and merging more nextflow-y

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• Post release version bup

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• Merge pull request #501 from nf-core/post-release-bumpv

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Commits on Jun 25, 2024

• remove dump from profiling.nf

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• Merge pull request #466 from LilyAnderssonLee/add_db_type

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Commits on Jul 2, 2024

• add output files to tower.yml

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• update changelog

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• delete non-supported files in tower.yml

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• delete big txt or tsv files from tower.yml

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• update changelog

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• update tower.yml

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• Merge pull request #505 from LilyAnderssonLee/add_files_tower

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Commits on Jul 11, 2024

• Add nanoq to the pipeline

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• Merge branch 'bouncy-basenji' into nanoq

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• update the module nanoq

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• update modules.config

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Commits on Jul 12, 2024

• Update nextflow_schema.json

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• Update subworkflows/local/longread_filtering.nf

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• Update subworkflows/local/longread_preprocessing.nf

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• Add nanoq to docs

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Commits on Jul 18, 2024

• Merge branch 'dev' into bouncy-basenji

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• Merge branch 'bouncy-basenji' of github.com:nf-core/taxprofiler into bouncy-basenji

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• add help text to longread_filter_tool

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• default of longread_filter_tool into nanoq in nextflow.config

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• Merge branch 'bouncy-basenji' into nanoq

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• remove nanoq from multiqc_config.yml

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• Merge pull request #508 from genomic-medicine-sweden/nanoq

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Commits on Jul 31, 2024

• Add porechop_abi to the pipeline

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• update changelog.md

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• add porechop_abi to multiqc report

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• update comments in longread_preprocessing.nf

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Commits on Aug 1, 2024

• modify porecho_abi module and add patch file

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• run lint

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• update modules

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• update ganon malt motus

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• Update assets/multiqc_config.yml

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• Merge pull request #511 from genomic-medicine-sweden/porechop_abi

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• update filtlong,ganon,krakentools

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Commits on Aug 8, 2024

• update bracken

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• add diamond warning for paired-end reads

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Commits on Aug 9, 2024

• Remove and consolidate duplicated emit

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• Merge pull request #514 from nf-core/fix-dup-emit

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• update krona,nonpareil and krakentools

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Commits on Aug 11, 2024

• Update Nonpareil to latest, add native MultiQC support, update output docs, fix MultiQC methods section

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• Fix rendering

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• Merge pull request #515 from nf-core/update-nonpareil

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Commits on Aug 27, 2024

• update metaphlan to the lastest

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• Merge branch 'bouncy-basenji' into update_tools

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Commits on Aug 28, 2024

• Update Multiqc to the latest

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Commits on Aug 30, 2024

• Add nanoq in the multiqc report

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• Fix bug where Nanopore FASTA files would be picked up into the FASTQ branch and thus not passed into the right FASTA channels

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• Use Ida's GH handle

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• update motus/profile

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• Merge pull request #518 from nf-core/fix-nanopore-fasta

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• Merge branch 'nf-core:master' into update_tools

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• separate fasta into fasta_shrt and fasta_long

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• Update changelog

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• add nanoq is default option to the usage

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• unique check for fasta file names

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• state that the pipeline is built on nextflow to README.md

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• update modules

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• Merge pull request #512 from genomic-medicine-sweden/update_tools

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• Remove porechop_abi patch

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• Fix patches on PORECHOP modules

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• Fix formatting

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• replace output-lca into -m lca in ganon classify

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• Drop unnecesary ganon parameter (should come via db_params) and pattern for classify to 2.0 valid,

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• Update output docs

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• Merge pull request #519 from nf-core/bouncy-basenji

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• bump version to 1.2

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• Merge pull request #524 from nf-core/pre-release-vbump

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Commits on Sep 12, 2024

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• Add nanoq and filtlong to alternative test profile for alternative short-read prep

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• Fix linting

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• Update tubemap

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• Rename test profile, update all databases to test to 1.2

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• Update all the other databases too

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• Update after suggestions from @sofstam

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• Fix linting

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• Additional minor fixes from @jfy133's review

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• Merge pull request #527 from nf-core/tubemap-update

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